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Refining the table of polytomous result #19

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abhisheksinghnl opened this issue Sep 26, 2016 · 13 comments
Open

Refining the table of polytomous result #19

abhisheksinghnl opened this issue Sep 26, 2016 · 13 comments

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@abhisheksinghnl
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Hi,

I have applied the polytomous analysis on my dataset consisting of 7 groups and each group with a replicate. The results are in a tabular form for all the genes.

I would like to know on the basis of which column shall I sort or filter to get the signature genes for each group.

Thank you.
Best regards
Abhishek
@eturro
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eturro commented Sep 26, 2016

Have you read in the 6 mmdiff comparison files using the polyclass() R function?

If so then you should have a posterior probability column in the table returned by that function, which you can rank on.

You should find that if you plot the "mu"s for the features with high posterior probabilities, you observe strong evidence of clustering within groups

The "eta" columns will tell you for each group whether it is up or down regulated relative to the global mean

bw
Ernest

On 26 Sep 2016, at 12:48, abhisheksinghnl notifications@github.com wrote:

Hi,

I have applied the polytomous analysis on my dataset consisting of 7 groups and each group with a replicate. The results are in a tabular form for all the genes.

I would like to know on the basis of which column shall I sort or filter to get the signature genes for each group.

Thank you.
Best regards
Abhishek

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@abhisheksinghnl
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Hi Ernest,

Yes, indeed I havres1=polyclass(files=c("E18vsOthers.mmdiff",
"P1vsOthers.mmdiff",
"P3vsOthers.mmdiff","P10vsOthers.mmdiff","Mo3vsOthers.mmdiff","Mo12vsOthers.mmdiff","Mo24vsOthers.mmdiff"),
prior=c(0.79,0.03,0.03,0.03,0.03,0.03,0.03,0.03))e read in all the seven
files and used this command:

res1=polyclass(files=c("E18vsOthers.mmdiff", "P1vsOthers.mmdiff",
"P3vsOthers.mmdiff","P10vsOthers.mmdiff","Mo3vsOthers.mmdiff","Mo12vsOthers.mmdiff","Mo24vsOthers.mmdiff"),
prior=c(0.79,0.03,0.03,0.03,0.03,0.03,0.03,0.03))

However, I do not get the eta column in my output file.

I have attached few lines of my out put file for your reference.

Please guide, thank you,

Best regards
Abhishek

On Mon, Sep 26, 2016 at 3:41 PM, Ernest Turro notifications@github.com
wrote:

Have you read in the 6 mmdiff comparison files using the polyclass() R
function?

If so then you should have a posterior probability column in the table
returned by that function, which you can rank on.

You should find that if you plot the "mu"s for the features with high
posterior probabilities, you observe strong evidence of clustering within
groups

The "eta" columns will tell you for each group whether it is up or down
regulated relative to the global mean

bw
Ernest

On 26 Sep 2016, at 12:48, abhisheksinghnl notifications@github.com
wrote:

Hi,

I have applied the polytomous analysis on my dataset consisting of 7
groups and each group with a replicate. The results are in a tabular form
for all the genes.

I would like to know on the basis of which column shall I sort or filter
to get the signature genes for each group.

Thank you.
Best regards
Abhishek

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.

"feature_id" "mu_E18_1.namesorted.bam.hits.gene" "mu_E18_2.namesorted.bam.hits.gene" "mu_E18_3.namesorted.bam.hits.gene" "mu_E18_4.namesorted.bam.hits.gene" "mu_P1_1.namesorted.bam.hits.gene" "mu_P1_2.namesorted.bam.hits.gene" "mu_P1_3.namesorted.bam.hits.gene" "mu_P3_1.namesorted.bam.hits.gene" "mu_P3_2.namesorted.bam.hits.gene" "mu_P3_3.namesorted.bam.hits.gene" "mu_P10_1.namesorted.bam.hits.gene" "mu_P10_2.namesorted.bam.hits.gene" "mu_P10_3.namesorted.bam.hits.gene" "mu_Mo3_1.namesorted.bam.hits.gene" "mu_Mo3_2.namesorted.bam.hits.gene" "mu_Mo3_3.namesorted.bam.hits.gene" "mu_Mo3_4.namesorted.bam.hits.gene" "mu_Mo12_1.namesort.bam.hits.gene" "mu_Mo12_2.namesort.bam.hits.gene" "mu_Mo12_3.namesort.bam.hits.gene" "mu_Mo12_4.namesort.bam.hits.gene" "mu_Mo24_1.namesort.bam.hits.gene" "mu_Mo24_2.namesort.bam.hits.gene" "mu_Mo24_3.namesort.bam.hits.gene" "mu_Mo24_4.namesort.bam.hits.gene" "mu_Mo24_5.namesort.bam.hits.gene" "mu_Mo24_6.namesort.bam.hits.gene" "mu_Mo24_7.namesort.bam.hits.gene" "postprob_model0" "postprob_model1" "postprob_model2" "postprob_model3" "postprob_model4" "postprob_model5" "postprob_model6" "postprob_model7"
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"ENSRNOG00000002989.6" 2.25403 1.98002 1.96921 1.66696 2.11155 2.27846 1.75942 2.0686 2.32693 2.21846 2.57585 1.98419 2.38291 2.78358 2.85638 2.46559 2.57641 2.58216 2.71846 2.74012 2.82205 2.58566 2.92111 7.07056 2.69686 2.73853 2.67528 2.76289
"ENSRNOG00000017297.7" 1.65408 1.98508 1.93102 1.70342 1.75404 2.06435 1.75834 1.80653 1.96784 1.91998 1.96023 1.70219 1.93469 1.81908 1.4911 1.81102 1.80478 1.60924 1.28469 1.44047 1.34826 1.79063 0.676179 6.89266 1.35183 1.30059 1.52613 1.6029
"ENSRNOG00000021131.6" 0.856163 1.17154 0.639029 1.12325 1.23698 1.39115 1.0504 1.25255 1.67255 1.76839 1.61036 1.69226 1.82739 1.94439 1.8786 1.8761 1.64717 1.84081 1.39995 1.66398 1.71608 1.30677 1.83929 -2.72083 1.6841 1.59238 1.44658 1.76516
"ENSRNOG00000052391.1" 1.18528 1.3196 1.60536 1.78342 2.01949 1.99642 2.37501 2.41484 2.26283 2.21932 2.13215 2.54861 2.67611 2.79479 2.57159 2.64787 2.14862 2.47213 2.39064 2.39403 2.32429 2.27815 2.52874 -3.24489 2.30282 2.2781 2.18554 2.4905
"ENSRNOG00000011307.7" 3.16992 2.92901 2.81443 3.18604 3.11792 3.35112 2.79676 3.51469 3.60141 3.56456 3.80201 3.72718 3.95761 3.98893 3.98653 3.91656 3.42214 3.7157 3.59235 3.36354 3.48988 3.10165 3.56209 7.59483 3.59337 3.60686 3.33752 3.41514
"ENSRNOG00000010887.6" -0.585553 -1.01894 -0.0496335 -0.471697 -0.843725 -0.481059 -0.300618 0.5759 -0.195396 0.146203 0.0796976 0.0642451 -0.535319 0.629151 0.67259 0.863107 0.64814 0.650888 0.36257 0.501463 0.384773 -1.29147 0.69403 6.94143 0.457878 -0.220791 0.299694 -0.480542
"ENSRNOG00000023187.6" 1.46504 0.887183 1.24552 1.61005 1.09467 1.26126 0.418396 1.53368 0.855762 0.932614 0.366172 0.759945 1.24844 1.12629 1.25751 0.933387 1.16129 1.14958 0.803886 0.864796 1.24077 1.28881 0.335357 -2.75406 1.06437 1.16327 0.817925 0.979882
"ENSRNOG00000057756.1" 1455 1.32063 1.62799 1.27712 1.65206 1.46164 1.48063 1.7734 1.59474 1.59433 1.86442 2.04148 1.94293 2.2184 2.25856 2.0022 1.92134 2.14297 1.90615 2.16301 1.66144 1.79073 2.4173 -3.09527 2.08229 2.02341 1.94261 1.81776
"ENSRNOG00000007290.6" 1.44677 1.20292 1.33589 1.67063 1.14331 1.28442 1.55201 1.21844 1.28787 1.53014 2.47805 2.03863 2.12958 3.6053 3.56493 3.28956 3.2289 3.09063 3.49819 3.3699 3.18551 2.91746 3.39962 6.53004 3.48938 3.41588 3.02416 3.12295
"ENSRNOG00000016603.6" 0.545314 0.53067 0.309988 0.325372 0.956843 0.604619 0.683474 1.29088 0.849632 1.12065 1.31293 1.1092 1.27542 1.11472 1.11564 1.39888 1.41987 1.10706 0.932786 1.27715 1.01573 -1.09682 0.315893 -3.18839 1.25639 0.94107 0.593975 0.598872
"ENSRNOG00000011645.4" 1.89132 1.52782 1.11049 1.5786 1.93429 1.91948 1.34514 1.68877 1.85516 1.92896 1.83837 1.96002 1.99957 2.14437 2.10559 2.18168 1.73298 2.10345 2.20523 1.80278 1.7656 2.06285 1.97804 -3.36909 2.0471 1.82168 1.70354 1.72046
"ENSRNOG00000008825.6" 3.12276 2.88741 2.74496 2.67208 2.70192 2.65875 2.63093 2.28459 2.62609 2.67934 2.13917 2.62762 2.37276 2.00599 1.89098 1.82786 1.48708 1.98146 1.89744 1.72061 1.92335 2.68325 2.29286 2.14002 1.98888 1.90579 1.8958 1.97172
"ENSRNOG00000053510.1" 2.05882 1.92468 1.97224 2.24006 2.17163 2.45313 2.35473 2.24797 2.03016 2.13942 1.72852 1.93947 2.02674 1.82505 2.00058 1.80376 1.68313 1.61746 1.72056 1.68711 1.17552 2.57188 1.39552 7.09066 1.37448 1.43623 1.71286 1.81074
"ENSRNOG00000053054.1" 0.923223 1.65779 1.21904 1.13075 1.54262 1.38773 1.45361 1.50068 1.35223 1.00688 0.868094 509 0.8979 1.39271 1.14273 0.498758 0.87645 0.970768 0.902446 1.03319 1.11827 -10.1114 -8.61003 -3.26393 1.04765 1.01738 1.29388 1.30208
"ENSRNOG00000001719.6" 2.18814 2.15084 2.55627 1.88079 1.97894 1.98165 2.31524 1783 2.00042 1.91009 2.2148 2.30951 2.23006 2.31787 2.28514 2.06504 2.16613 2.14835 2.21201 1.91709 2.13415 0.7823 1.70276 6.91323 2.07883 2.09098 1.96694 2.0803
"ENSRNOG00000023816.5" 2.42428 2.7084 2.72237 2.50094 2.44861 2.61601 2.4563 2.66614 2.6791 2.33391 2.40791 2.48576 2.18484 2.92346 2.76207 2.91103 3.04268 2.74608 3.31793 3.01098 3.04895 2.34268 1.19064 2.16959 3.05867 3.21608 2.89946 2.98609
"ENSRNOG00000054725.1" 1.11114 1.34045 1.3753 1.17179 1.34699 1.42992 1.09662 1.07789 1.30174 1.23391 1.37625 1.27542 1.09541 1.15933 1.26415 1.44893 1.18419 0.911578 1.10115 1.07015 1.16962 1.06171 1.71895 -4.03337 1.15111 1.16114 1.11053 1.1304
"ENSRNOG00000060542.1" 0.205079 0.35632 0.401772 0.211656 0.276147 0.686359 -0.185559 0.594354 -0.0525686 0.240618 0.450178 -0.0650879 0.469802 0.493494 0.61885 0.705907 0.605394 0.361383 0.22403 0.397671 0.387778 1.12416 -0.388024 -3.03683 0.492242 0.226974 0.658775 0.344635
"ENSRNOG00000037707.3" 0.829163 0.975113 0.917112 0.807838 0.901903 0.731999 1.29432 0.725268 0.682132 0.221199 0.587994 0.431968 0.440512 0.250355 0.171091 0.0300642 -0.358257 0.303551 -0.369599 0.339324 -0.267024 -11.1196 0.489735 -2.84753 -0.233153 0.444108 -0.235744 -1.08042
"ENSRNOG00000014305.7" 1.6081 1.72722 1.66303 1.4377 1.57664 1.47439 1712 1.64266 1.7607 1.4575 1.75519 1.86036 1.86533 1.80577 1.39875 1.59836 1.54264 1.22599 1.34147 1.32799 1.25351 2.5038 1.59755 1.96192 1.26149 1.44481 1.30544 1.24988
"ENSRNOG00000016973.6" 1.1453 1.08634 1.41345 1.29456 0.898413 0.635569 1.06992 1.72908 1.12528 1.24921 1.19641 1.0122 1.47418 1.59139 2.01154 2.20718 1.54937 1.53098 1.41925 1.57627 1.69563 -10.4252 -0.680677 -2.54005 0.791649 1.48479 1.20628 1661
"ENSRNOG00000010257.7" 1.77941 1.66151 1.44716 1.67091 1.61891 2.02205 2.07258 1.8405 2.11003 1.91138 2.18129 2.1462 2.41867 2.76483 2.65593 2.4774 2.7082 2.36343 2.62119 2.33065 2.58126 3.38187 2.80907 -2.57872 2.58896 2.52369 2.20523 2.37566
"ENSRNOG00000009104.6" 0.646474 0.46135 0.485874 0.959248 0.747253 0.473572 0.582947 0.592558 0.315518 0.628284 0.325429 0.622977 0.81016 0.753701 1.08115 0.773757 1.32512 1.11366 0.851516 1.08188 1.31878 0.99925 0.871999 -3.04644 0.728567 0.95317 1.18871 1.41979
"ENSRNOG00000011262.6" 2.33662 2.40311 2.2088 1.82944 2.41875 2.16581 2.30808 1.55262 2.98449 2.5381 3.15792 3.05902 3.13695 3.04718 3.05374 3.14659 2.71975 2.6132 2.65611 2.51301 2.48123 2.96119 2.97002 -3.52333 2.91249 2.69476 2.43692 2.60351
"ENSRNOG00000006063.8" 1.7681 1.80761 1.70656 1.60117 1.84972 1.48839 2.37108 1.59166 1.74359 1.61463 1.74975 1.64425 1.68494 2.07214 2.00656 1.80758 1.77517 1.60158 1.43626 1.45878 1.62423 1.8497 2.38042 6.9864 1.36194 1.53492 1.60846 1.47662
"ENSRNOG00000027238.3" 0.17634 0.825493 0.573963 0.638778 0.971023 0.652409 1.22923 0.768228 0.740722 1.00845 1.10933 1.00797 1.00488 1.38545 1.06207 1.38363 1.04101 1.08938 1.11432 0.836546 1.10328 2.04232 0.538772 -2.56567 1.13502 1.37325 0.836055 0.942382
"ENSRNOG00000028941.3" 0.717182 0.657303 1.21846 0.146784 0.591613 0.675269 1.23935 0.510279 0.662212 0.362605 0.871204 0.411831 0.524572 -0.499658 0.17825 -0.146087 -0.659073 -0.191457 -0.110617 -0.4714 -1.01637 -10.7507 -11.6902 -2.62276 -0.624774 -0.534965 -0.259332 -1.01986
"ENSRNOG00000038766.3" 1.28423 1.50941 1.62886 0.976258 1.65245 1.43822 1.85751 1.50101 1.88178 1.51414 1.51146 1.21353 1.27886 1.54916 1.42282 1.47992 1.05635 1.16502 0.553141 1.08428 0.951361 1.79845 0.418606 -2.96898 0.740094 0.87782 0.998445 0.748212
"ENSRNOG00000010218.7" 2.23963 2.18599 2.20471 2.60305 2.14771 2.25757 1.88427 2.12937 1.87912 2.10474 1.65526 2.08127 2.07798 1.9738 2.13598 1.88127 2.54362 2.28036 1.82434 2.07782 2.29213 1.37739 2.10596 0.512681 2.01732 2.10257 2.42725 2.23939
"ENSRNOG00000033624.3" 1.75014 1.3507 1.12974 1.52375 1.54695 1.30507 0.531626 1.30776 1.61354 1.58727 1.41234 1.38828 1.3456 1.59678 1.97411 1.61522 1.85027 1.9717 1.77515 1.73691 1.73354 1.95234 2.53115 2.20445 2.00956 1.89268 1.82348 1.55955
"ENSRNOG00000003226.8" 3.32882 3.42043 3.23032 3.01865 3.43609 3.07698 3.6206 3.24643 3.38719 3.32762 3.49002 3.72414 3.61658 3.31882 3.38072 3.31579 2.88093 2.98599 2.96451 2.91802 2.74692 3.92968 3.59059 6.79026 3.08264 3.0131 2.70516 2.8931
"ENSRNOG00000047014.3" 1.52486 1.56381 1.63335 1.9762 1.43879 1.69649 1.33879 1.65828 1.98354 2.12235 2.31801 1.87241 2.57566 2.92732 2.90014 2.53611 2.71277 2.49405 2.26577 2.39251 2.51274 1.7929 2.69967 4.13304 2.30838 2.22452 2.58073 2.4946
"ENSRNOG00000014380.6" 0.267594 0.370753 0.586828 0.898008 0.261106 0.308237 -0.0685143 0.423922 -0.13057 0.247062 0.342391 0.105265 0.588703 0.305369 0.71213 0.28991 1.26815 0.938908 0.196242 0.782696 0.937571 -11.3411 0.501828 -3.1764 0.418946 0.81613 0.807045 0.812632
"ENSRNOG00000048577.2" 0.961083 1.17856 1.18365 1.93981 1.39136 1.86793 0.803332 1.62809 1.03593 1.14028 1.23753 1.05723 1.23275 0.954371 1.37493 1.2848 1.40784 1.54376 1.18943 1.45473 1.8012 -0.898888 1.07858 4.50101 1.19262 1.41352 1.88882 1.6475
"ENSRNOG00000049724.3" 1.6932 1.53929 1.76654 2.11992 1.75368 1.77623 0.723253 1.74233 1.64252 1.65328 1.82848 1.76485 1.78277 2.76846 2.54647 2.51925 2.39297 2.83235 2.63664 2.70883 2.45044 0.896408 3.1109 7.20928 2.71462 2.49579 2.43641 2.63836
"ENSRNOG00000029416.5" -0.433591 0.318168 -0.403574 0.233917 0.221847 0.366425 0.508874 0.362818 -0.0256196 -0.126019 0.724224 0.267111 0.82231 0.783001 0.59767 0.565547 1.30791 1.31612 0.663015 1.45188 1.10078 0.162211 1794 -3.16109 1.18383 1.23818 1.21205 0.872662
"ENSRNOG00000037165.5" 0.644098 0.634013 0.258783 1.04189 0.948443 1.09316 0.0194727 1.08225 1.64037 0.791034 1.55445 1.92471 1.95441 1.57593 2.21347 1.51511 1.63657 2.17605 2.27169 2.09834 1.73701 -11.3315 2.75607 -2.76535 2.28977 2.31695 1.89708 2.04541
"ENSRNOG00000021380.5" -0.546586 -0.138967 -0.247293 0.00840186 0.115794 0.912879 -0.544706 -0.14335 0.800102 0.599864 1.16515 1.45582 1.39625 2.16054 1.85061 2.19581 1.24252 1.49206 1.40378 1.52638 1.45802 0.963892 1.50657 -2.47552 1.61768 1.4684 1.66985 1.2523
"ENSRNOG00000057851.1" 0.829663 1.00953 1.17392 1.64837 0.912653 0.220613 0.279506 1.38686 0.760282 1.36296 0.241133 -0.294389 0.138105 0.789291 0.86362 0.785437 1.18593 0.631868 1.56422 1.43352 1.61167 -10.3464 -0.942527 -2.89857 1.05212 1.00484 1.28111 1.42318
"ENSRNOG00000020651.7" 1.2702 1.17416 1.36428 0.951488 1.08842 0.962329 1.40488 1.02372 0.772682 0.854994 0.671484 0.944946 0.96339 0.963181 0.7739 0.722817 0.701833 0.865988 0.786516 0.736166 0.760171 1.95121 1.8138 -3.19861 0.974428 0.90686 0.769205 0.628872
"ENSRNOG00000003479.6" 0.461476 0.702273 0.548115 0.748578 1.01254 1.05293 1.18023 1.49358 1.50482 1.76689 2.07712 1.82295 1.91292 2.01207 2.2743 2.03457 1.36363 1.82158 1.69652 1.59104 1.44211 1.75314 1.80512 -3.3785 1.67128 1.4459 1.55921 1.42373
"ENSRNOG00000013195.6" 1.44333 1.46559 1.79886 0.764538 0.887133 1.00769 1.50284 0.804098 1.08967 0.817914 0.880264 0.249708 0.366649 0.294753 0.539339 0.164575 0.85961 0.0120629 0.506542 0.0177814 0.217875 0.202047 -0.600287 2.28518 0.672657 0.405606 0.417542 0.320589
"ENSRNOG00000039496.2" 2.48424 2.59575 2.8313 2.72401 2.36586 2.4196 2.86654 2.25591 1.65883 2.25775 1.6042 1.14698 0.92432 0.898941 1.12452 1.3869 1.56054 1.53282 1.86527 2.15151 1.95073 -10.4198 -1.07216 -2.90181 1.62649 1992 2.12717 2.34106
"ENSRNOG00000009412.6" 2.01366 1.99078 1.69471 2.21405 2.27751 2.5551 1.97819 2.26394 2.47468 2.25632 2.43086 2.7138 2.73147 2.43544 2.55202 2.22321 1.97247 2026 1.9955 1.94764 1.96471 2.85676 2.42135 6.84316 2.09559 2.01264 1.59807 1.87134
"ENSRNOG00000032134.4" 3.18508 3.12746 3.69746 3.09021 3.11796 3.62978 3.98574 3.21761 3.30266 3.53253 3.35397 3.87257 3.6995 3.91613 3.86152 3.6926 3.49888 3.37227 3.46916 3.47077 3.46628 3.35655 3.45213 7.15107 3.43357 3.26077 3.20389 3.26164
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"ENSRNOG00000014270.4" 2.13043 1.93631 2.17142 1.73056 1.73271 2.20849 1.97261 1.86924 1.36414 1.79335 1.51614 1.39374 0.99956 1.10068 1.01519 0.846567 1.17577 0.891188 1.0919 1.00923 1.53193 1.32242 1.33878 7.23473 1.01124 0.96812 1.28323 1.48874
"ENSRNOG00000014284.5" 0.734797 1.06184 1.59195 0.358771 0.056033 0.136241 0.556655 0.408303 0.485922 0.588404 0.633824 0.655131 -0.431787 -1.04252 -0.3868 0.254604 -1.06055 -0.126576 0.314569 0.379808 -0.692053 -0.494018 0.180635 -2.18135 -0.0443678 0.0235216 -0.501026 0.513477
"ENSRNOG00000014311.5" -0.14024 -0.221935 -0.028666 0.569718 -0.00890596 -0.416196 0.349359 -0.356139 -0.310759 -0.463595 0.160878 -0.631981 -0.489006 0.0538892 0.082097 0.270299 0.96295 0.3033 0.755115 0.550786 1.02117 0.639291 1.14546 1.95111 0.976638 0.527857 0.824445 0.723642
"ENSRNOG00000014475.4" 1.55946 1.69877 1.76235 1.29883 1.05941 1.38628 1.04452 1.13701 0.658832 1.03001 0.748904 0.258826 0.0803571 0.893431 0.171207 0.544407 -0.255203 -0.12444 0.015108 0.314923 0.596651 0.147218 -12.2676 -2.65649 -0.336677 0.512818 0.702075 0.943372
"ENSRNOG00000014493.6" 1.9313 1.88834 1.71906 1.86692 1.91421 1.91317 1.46825 1.84073 1.79665 1.81669 2.25499 1.78626 2.03065 1.84961 1.96613 2.33046 1.74227 2.18668 1997 2.18119 2.20311 2.49169 2.71337 7.30519 2.20724 2.0826 2.15583 2.00961
"ENSRNOG00000014635.8" 2.43607 2.3505 2.54051 1.55581 2.17753 2.42901 2.4042 2.14336 2.3436 2.44106 2.36733 2.35154 2.25091 2.16792 2.48116 2215 1.67609 1.80052 1.95122 1.45929 1.8699 1.71539 2.01911 7.49104 1.94966 1.94622 1.75962 1.55369
"ENSRNOG00000014675.2" 1.71631 1.81465 1.69236 1.85414 1.72651 2.30461 1.17568 1.58562 2.08749 2.03224 2.41698 2.30871 2.51251 3.41429 3.25237 3.07091 2.91198 2.91356 2.85482 2.74492 2.57449 3.03542 2.8867 8.04614 2.78742 2.54481 2.41897 2.44291
"ENSRNOG00000014828.5" 1.01656 0.787273 1.51834 1.05225 1266 1.65303 1.82163 1.85523 0.969592 1.34867 1.80952 1.20396 0.793441 1.27798 0.553838 0.839437 1.19264 1.1212 1.53181 1.51211 1.41858 1.26145 -11.1765 -3.53349 1.08677 1.17417 1.20366 1.47794
"ENSRNOG00000015117.5" 1.8483 1.64694 1.71835 2.35804 2.3084 2.43547 1.66588 2.03523 2.43196 2.57631 2.55427 2.71714 2.56381 2.52626 2.52519 2.72191 2.88195 2.8362 2.35056 2.41598 3.12081 -0.545688 2.69023 -2.92339 2.40581 2.1944 2.77586 2.35077
"ENSRNOG00000015142.4" 1.21368 0.872133 1.61173 0.969598 0.462713 1.12661 -0.703009 1.0907 0.625932 0.790624 0.826364 0.340733 0.574859 0.757031 0.89797 0.541237 0.91918 1.27873 1.0219 1.24934 1.25887 -10.5604 0.327821 -2.70676 0.723775 0.785439 1.17436 0.979792
"ENSRNOG00000015255.6" 0.635166 1.09467 0.960959 1.23027 0.831073 1.59706 0.60128 1.09024 0.787662 1.31644 -0.570947 0.256745 0.389404 -0.644887 -1.21314 -0.77266 -0.342358 -0.209389 -0.789478 -0.546111 -0.0696438 0.572373 -12.1533 -3.27651 -0.288691 0.247212 0.063807 -0.0788222
"ENSRNOG00000015271.7" 0.34225 -0.0864621 -0.420396 0.947378 0.22373 0.646939 0.334785 0.600073 0.126738 0.214864 0.301494 -0.701341 -0.329095 0.23911 0.495603 0.404036 0.484115 0.689228 0.704947 0.670936 0.742831 0.659101 0.905933 1.90036 0.766806 0.667169 0.933665 0.842992
"ENSRNOG00000015488.7" 3.45224 3.30972 3.1981 3.16098 3.53076 3.61891 3.31948 3.4722 3.89426 3.73517 3.58889 3.76377 3.73657 3.9276 4.1647 3775 3.1758 3.52078 3.25142 3.47916 3.52366 3.87992 4.2406 7.27741 3.33201 3.22192 3.22409 3.27264
"ENSRNOG00000015718.5" -0.604849 -0.914111 -1.37528 -0.514172 -0.533857 -0.153083 -7.3498 -1.37349 0.346189 -0.0866821 0.417644 -0.380773 0.203298 0.915931 0.148214 0.820207 0.559821 0.811228 1.50097 1.01426 1.10617 -6.61361 0.889786 1.94846 1.34223 1.24974 1.10228 1.17295
"ENSRNOG00000015762.6" 1.2063 1.13676 1.24927 1.01618 1.49932 1.40316 1.76073 1.41854 1.97302 1.67342 2.00881 2.47602 2.70518 2.41738 2.21105 2.22312 2.11051 2.06415 2.29378 2.0739 1.97781 3.05224 2.69214 -2.74887 2.17244 2.07997 1.74751 1.79987
"ENSRNOG00000016419.6" 4.65628 4.34215 4.32164 4.71946 4.24845 4.55401 3.28134 4.66389 4.76392 4.49844 4.23584 4.45005 4.47171 4.08861 4.03635 4.00244 3.64525 3.78828 3.80917 3.70173 4.2819 2.30077 3.94221 7.11331 4.02926 3.90942 3.6551 3.83098
"ENSRNOG00000016707.7" 2.38271 2.1257 1.67641 2.29899 2.45845 2.46275 1.95709 2.18669 2.45143 2.6633 1.98445 2.59569 2.39227 1.68757 1.83501 1.46113 1.80801 1.86123 1.6672 1.85959 1.31671 2.85633 2.04767 1.94404 1.93301 1.51374 1.93368 1.63786
"ENSRNOG00000017057.7" 2.33222 2.26903 1.57957 1.99659 2.36802 2.10216 2.87728 2.30981 2.54491 1.97659 2.44641 2.78393 2.45185 2.74208 2.45314 2.33028 2.3304 2.46126 2.25471 2.07947 2.28284 3.30166 2.46714 -2.35308 2.23172 2.24431 2.26424 2.26756
"ENSRNOG00000017631.4" 1.54478 1.42706 0.974302 1.75373 1.41059 1.25239 1.5975 1.35758 1018 1.46692 1.02534 1.17147 1.67823 1.3923 1.84478 1.63548 2.12553 1.92622 1.95872 1.88998 2.19532 -0.183199 1.90119 7.05053 1.87483 2.04449 1.85215 1.63556
"ENSRNOG00000017720.5" 1.14253 1.2849 1.22687 0.741418 1.16879 0.776949 1.25031 0.393884 1.30452 1.2

@eturro
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eturro commented Sep 26, 2016

That looks fine

postprob_model0 is the posterior probability of the baseline model (global mean, I assume)
postprob_model1-7 are the probabilities for each of the seven models.

The "mu" values are the estimated log expression values

You're right that the etas are not read in but you can find them in the *mmdiff files if you need them

Best wishes
Ernest

On 26 Sep 2016, at 14:47, abhisheksinghnl notifications@github.com wrote:

Hi Ernest,

Yes, indeed I havres1=polyclass(files=c("E18vsOthers.mmdiff",
"P1vsOthers.mmdiff",
"P3vsOthers.mmdiff","P10vsOthers.mmdiff","Mo3vsOthers.mmdiff","Mo12vsOthers.mmdiff","Mo24vsOthers.mmdiff"),
prior=c(0.79,0.03,0.03,0.03,0.03,0.03,0.03,0.03))e read in all the seven
files and used this command:

res1=polyclass(files=c("E18vsOthers.mmdiff", "P1vsOthers.mmdiff",
"P3vsOthers.mmdiff","P10vsOthers.mmdiff","Mo3vsOthers.mmdiff","Mo12vsOthers.mmdiff","Mo24vsOthers.mmdiff"),
prior=c(0.79,0.03,0.03,0.03,0.03,0.03,0.03,0.03))

However, I do not get the eta column in my output file.

I have attached few lines of my out put file for your reference.

Please guide, thank you,

Best regards
Abhishek

On Mon, Sep 26, 2016 at 3:41 PM, Ernest Turro notifications@github.com
wrote:

Have you read in the 6 mmdiff comparison files using the polyclass() R
function?

If so then you should have a posterior probability column in the table
returned by that function, which you can rank on.

You should find that if you plot the "mu"s for the features with high
posterior probabilities, you observe strong evidence of clustering within
groups

The "eta" columns will tell you for each group whether it is up or down
regulated relative to the global mean

bw
Ernest

On 26 Sep 2016, at 12:48, abhisheksinghnl notifications@github.com
wrote:

Hi,

I have applied the polytomous analysis on my dataset consisting of 7
groups and each group with a replicate. The results are in a tabular form
for all the genes.

I would like to know on the basis of which column shall I sort or filter
to get the signature genes for each group.

Thank you.
Best regards
Abhishek

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"feature_id" "mu_E18_1.namesorted.bam.hits.gene" "mu_E18_2.namesorted.bam.hits.gene" "mu_E18_3.namesorted.bam.hits.gene" "mu_E18_4.namesorted.bam.hits.gene" "mu_P1_1.namesorted.bam.hits.gene" "mu_P1_2.namesorted.bam.hits.gene" "mu_P1_3.namesorted.bam.hits.gene" "mu_P3_1.namesorted.bam.hits.gene" "mu_P3_2.namesorted.bam.hits.gene" "mu_P3_3.namesorted.bam.hits.gene" "mu_P10_1.namesorted.bam.hits.gene" "mu_P10_2.namesorted.bam.hits.gene" "mu_P10_3.namesorted.bam.hits.gene" "mu_Mo3_1.namesorted.bam.hits.gene" "mu_Mo3_2.namesorted.bam.hits.gene" "mu_Mo3_3.namesorted.bam.hits.gene" "mu_Mo3_4.namesorted.bam.hits.gene" "mu_Mo12_1.namesort.bam.hits.gene" "mu_Mo12_2.namesort.bam.hits.gene" "mu_Mo12_3.namesort.bam.hits.gene" "mu_Mo12_4.namesort.bam.hits.gene" "mu_Mo24_1.namesort.bam.hits.gene" "mu_Mo24_2.namesort.bam.hits.gene" "mu_Mo24_3.namesort.bam.hits.gene" "mu_Mo24_4.namesort.bam.hits.gene" "mu_Mo24_5.namesort.bam.hits.gene" "mu_Mo24_6.namesort.bam.hits.gene" "mu_Mo24_7.namesort.bam.hits.gene" "postprob_model0" "postprob_model1" "postprob_model2" "postprob_model3" "postprob_model4" "postprob_model5" "postprob_model6" "postprob_model7"
"ENSRNOG00000001293.6" 1.94281 1.99625 2.10187 1.99054 1.8606 2.00837 1.88069 1.71499 2.02734 2.12084 1.51931 1.8947 2.01762 1.3112 1.48374 1.2281 1.44441 0.968038 1.27799 1.26317 1.28953 1.87784 1.34061 7.05464 1.3488 1.25327 1.22406 1.18975
"ENSRNOG00000002989.6" 2.25403 1.98002 1.96921 1.66696 2.11155 2.27846 1.75942 2.0686 2.32693 2.21846 2.57585 1.98419 2.38291 2.78358 2.85638 2.46559 2.57641 2.58216 2.71846 2.74012 2.82205 2.58566 2.92111 7.07056 2.69686 2.73853 2.67528 2.76289
"ENSRNOG00000017297.7" 1.65408 1.98508 1.93102 1.70342 1.75404 2.06435 1.75834 1.80653 1.96784 1.91998 1.96023 1.70219 1.93469 1.81908 1.4911 1.81102 1.80478 1.60924 1.28469 1.44047 1.34826 1.79063 0.676179 6.89266 1.35183 1.30059 1.52613 1.6029
"ENSRNOG00000021131.6" 0.856163 1.17154 0.639029 1.12325 1.23698 1.39115 1.0504 1.25255 1.67255 1.76839 1.61036 1.69226 1.82739 1.94439 1.8786 1.8761 1.64717 1.84081 1.39995 1.66398 1.71608 1.30677 1.83929 -2.72083 1.6841 1.59238 1.44658 1.76516
"ENSRNOG00000052391.1" 1.18528 1.3196 1.60536 1.78342 2.01949 1.99642 2.37501 2.41484 2.26283 2.21932 2.13215 2.54861 2.67611 2.79479 2.57159 2.64787 2.14862 2.47213 2.39064 2.39403 2.32429 2.27815 2.52874 -3.24489 2.30282 2.2781 2.18554 2.4905
"ENSRNOG00000011307.7" 3.16992 2.92901 2.81443 3.18604 3.11792 3.35112 2.79676 3.51469 3.60141 3.56456 3.80201 3.72718 3.95761 3.98893 3.98653 3.91656 3.42214 3.7157 3.59235 3.36354 3.48988 3.10165 3.56209 7.59483 3.59337 3.60686 3.33752 3.41514
"ENSRNOG00000010887.6" -0.585553 -1.01894 -0.0496335 -0.471697 -0.843725 -0.481059 -0.300618 0.5759 -0.195396 0.146203 0.0796976 0.0642451 -0.535319 0.629151 0.67259 0.863107 0.64814 0.650888 0.36257 0.501463 0.384773 -1.29147 0.69403 6.94143 0.457878 -0.220791 0.299694 -0.480542
"ENSRNOG00000023187.6" 1.46504 0.887183 1.24552 1.61005 1.09467 1.26126 0.418396 1.53368 0.855762 0.932614 0.366172 0.759945 1.24844 1.12629 1.25751 0.933387 1.16129 1.14958 0.803886 0.864796 1.24077 1.28881 0.335357 -2.75406 1.06437 1.16327 0.817925 0.979882
"ENSRNOG00000057756.1" 1455 1.32063 1.62799 1.27712 1.65206 1.46164 1.48063 1.7734 1.59474 1.59433 1.86442 2.04148 1.94293 2.2184 2.25856 2.0022 1.92134 2.14297 1.90615 2.16301 1.66144 1.79073 2.4173 -3.09527 2.08229 2.02341 1.94261 1.81776
"ENSRNOG00000007290.6" 1.44677 1.20292 1.33589 1.67063 1.14331 1.28442 1.55201 1.21844 1.28787 1.53014 2.47805 2.03863 2.12958 3.6053 3.56493 3.28956 3.2289 3.09063 3.49819 3.3699 3.18551 2.91746 3.39962 6.53004 3.48938 3.41588 3.02416 3.12295
"ENSRNOG00000016603.6" 0.545314 0.53067 0.309988 0.325372 0.956843 0.604619 0.683474 1.29088 0.849632 1.12065 1.31293 1.1092 1.27542 1.11472 1.11564 1.39888 1.41987 1.10706 0.932786 1.27715 1.01573 -1.09682 0.315893 -3.18839 1.25639 0.94107 0.593975 0.598872
"ENSRNOG00000011645.4" 1.89132 1.52782 1.11049 1.5786 1.93429 1.91948 1.34514 1.68877 1.85516 1.92896 1.83837 1.96002 1.99957 2.14437 2.10559 2.18168 1.73298 2.10345 2.20523 1.80278 1.7656 2.06285 1.97804 -3.36909 2.0471 1.82168 1.70354 1.72046
"ENSRNOG00000008825.6" 3.12276 2.88741 2.74496 2.67208 2.70192 2.65875 2.63093 2.28459 2.62609 2.67934 2.13917 2.62762 2.37276 2.00599 1.89098 1.82786 1.48708 1.98146 1.89744 1.72061 1.92335 2.68325 2.29286 2.14002 1.98888 1.90579 1.8958 1.97172
"ENSRNOG00000053510.1" 2.05882 1.92468 1.97224 2.24006 2.17163 2.45313 2.35473 2.24797 2.03016 2.13942 1.72852 1.93947 2.02674 1.82505 2.00058 1.80376 1.68313 1.61746 1.72056 1.68711 1.17552 2.57188 1.39552 7.09066 1.37448 1.43623 1.71286 1.81074
"ENSRNOG00000053054.1" 0.923223 1.65779 1.21904 1.13075 1.54262 1.38773 1.45361 1.50068 1.35223 1.00688 0.868094 509 0.8979 1.39271 1.14273 0.498758 0.87645 0.970768 0.902446 1.03319 1.11827 -10.1114 -8.61003 -3.26393 1.04765 1.01738 1.29388 1.30208
"ENSRNOG00000001719.6" 2.18814 2.15084 2.55627 1.88079 1.97894 1.98165 2.31524 1783 2.00042 1.91009 2.2148 2.30951 2.23006 2.31787 2.28514 2.06504 2.16613 2.14835 2.21201 1.91709 2.13415 0.7823 1.70276 6.91323 2.07883 2.09098 1.96694 2.0803
"ENSRNOG00000023816.5" 2.42428 2.7084 2.72237 2.50094 2.44861 2.61601 2.4563 2.66614 2.6791 2.33391 2.40791 2.48576 2.18484 2.92346 2.76207 2.91103 3.04268 2.74608 3.31793 3.01098 3.04895 2.34268 1.19064 2.16959 3.05867 3.21608 2.89946 2.98609
"ENSRNOG00000054725.1" 1.11114 1.34045 1.3753 1.17179 1.34699 1.42992 1.09662 1.07789 1.30174 1.23391 1.37625 1.27542 1.09541 1.15933 1.26415 1.44893 1.18419 0.911578 1.10115 1.07015 1.16962 1.06171 1.71895 -4.03337 1.15111 1.16114 1.11053 1.1304
"ENSRNOG00000060542.1" 0.205079 0.35632 0.401772 0.211656 0.276147 0.686359 -0.185559 0.594354 -0.0525686 0.240618 0.450178 -0.0650879 0.469802 0.493494 0.61885 0.705907 0.605394 0.361383 0.22403 0.397671 0.387778 1.12416 -0.388024 -3.03683 0.492242 0.226974 0.658775 0.344635
"ENSRNOG00000037707.3" 0.829163 0.975113 0.917112 0.807838 0.901903 0.731999 1.29432 0.725268 0.682132 0.221199 0.587994 0.431968 0.440512 0.250355 0.171091 0.0300642 -0.358257 0.303551 -0.369599 0.339324 -0.267024 -11.1196 0.489735 -2.84753 -0.233153 0.444108 -0.235744 -1.08042
"ENSRNOG00000014305.7" 1.6081 1.72722 1.66303 1.4377 1.57664 1.47439 1712 1.64266 1.7607 1.4575 1.75519 1.86036 1.86533 1.80577 1.39875 1.59836 1.54264 1.22599 1.34147 1.32799 1.25351 2.5038 1.59755 1.96192 1.26149 1.44481 1.30544 1.24988
"ENSRNOG00000016973.6" 1.1453 1.08634 1.41345 1.29456 0.898413 0.635569 1.06992 1.72908 1.12528 1.24921 1.19641 1.0122 1.47418 1.59139 2.01154 2.20718 1.54937 1.53098 1.41925 1.57627 1.69563 -10.4252 -0.680677 -2.54005 0.791649 1.48479 1.20628 1661
"ENSRNOG00000010257.7" 1.77941 1.66151 1.44716 1.67091 1.61891 2.02205 2.07258 1.8405 2.11003 1.91138 2.18129 2.1462 2.41867 2.76483 2.65593 2.4774 2.7082 2.36343 2.62119 2.33065 2.58126 3.38187 2.80907 -2.57872 2.58896 2.52369 2.20523 2.37566
"ENSRNOG00000009104.6" 0.646474 0.46135 0.485874 0.959248 0.747253 0.473572 0.582947 0.592558 0.315518 0.628284 0.325429 0.622977 0.81016 0.753701 1.08115 0.773757 1.32512 1.11366 0.851516 1.08188 1.31878 0.99925 0.871999 -3.04644 0.728567 0.95317 1.18871 1.41979
"ENSRNOG00000011262.6" 2.33662 2.40311 2.2088 1.82944 2.41875 2.16581 2.30808 1.55262 2.98449 2.5381 3.15792 3.05902 3.13695 3.04718 3.05374 3.14659 2.71975 2.6132 2.65611 2.51301 2.48123 2.96119 2.97002 -3.52333 2.91249 2.69476 2.43692 2.60351
"ENSRNOG00000006063.8" 1.7681 1.80761 1.70656 1.60117 1.84972 1.48839 2.37108 1.59166 1.74359 1.61463 1.74975 1.64425 1.68494 2.07214 2.00656 1.80758 1.77517 1.60158 1.43626 1.45878 1.62423 1.8497 2.38042 6.9864 1.36194 1.53492 1.60846 1.47662
"ENSRNOG00000027238.3" 0.17634 0.825493 0.573963 0.638778 0.971023 0.652409 1.22923 0.768228 0.740722 1.00845 1.10933 1.00797 1.00488 1.38545 1.06207 1.38363 1.04101 1.08938 1.11432 0.836546 1.10328 2.04232 0.538772 -2.56567 1.13502 1.37325 0.836055 0.942382
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"ENSRNOG00000010728.6" 1.05243 1.35388 1.15515 1.09606 1.45105 1.79126 0.823009 1.56622 1.58686 1.65866 1.17805 1.45069 1.95663 1.66694 1.51104 1.77403 1.84124 1.57901 1.39257 1.57077 1.83733 -1.30709 1026 -3.11407 1.48309 1.44531 1.62103 1.48399
"ENSRNOG00000010849.5" 1.85328 1.56245 1.69585 1.42283 1.73755 1.48367 2.03423 1.51239 1.72462 1.87288 1.5912 1.83274 1.46296 1.58426 1.68937 1.68809 1.28843 1.29432 1.43148 1.33642 0.825991 1.52053 0.508939 7.16609 1.54434 1.71647 1.17708 1.38859
"ENSRNOG00000010930.6" 1.21427 1.08456 1.31031 1.01859 1.22856 1.67683 0.557495 1.36254 1.61118 1.7116 1.51854 1.86389 1.5785 1.78363 1.87669 1.35754 1.63563 1.65611 1.55913 1.67301 1.64649 1.48936 1.91615 6.93799 1.84988 1.84839 1.70005 1.51093
"ENSRNOG00000011146.6" 3.03603 3.01356 3.6033 3375 2.5607 2.95694 2.74997 3.09053 2424 2.57882 1.19434 1.23153 1.84852 1.88228 1.05857 1.57662 1.87391 1.03945 1.37017 1.48563 1.79285 -0.653178 0.517786 2.22202 1.0997 1.20523 1.7886 1.59329
"ENSRNOG00000011398.4" 0.553552 0.958393 0.796796 1.46062 0.778883 0.50109 0.921268 0.499798 0.730992 0.995534 0.926884 -0.470901 0.565655 1.48873 0.88734 0.906887 0.377499 0.719288 0.42395 -0.229473 0.2426 -3.94677 -0.185755 4.14226 0.805772 0.819378 0.626755 0.205597
"ENSRNOG00000011471.5" 0.314854 -0.0616441 -1.64266 0.722358 -0.122552 -0.553861 -0.0903673 0.418742 0.22567 -0.162916 -0.313735 -0.26876 -0.524615 0.10491 -0.467624 0.327976 0.003863 0.438369 0.143137 0.483323 0.0890582 -10.8985 0.105104 -2.66554 -0.0300438 0.165855 0.526795 0.184999
"ENSRNOG00000011509.7" 0.844193 0.886303 0.61881 0.990848 0.501003 1.22504 1.10223 0.814238 0.910652 0.973314 0.460101 1.0472 0.739422 1.05905 0.98189 0.928177 0.59579 1.26907 1.05395 0.930876 0.516561 0.930369 1.68809 -3.19161 1.29549 0.87537 0.576355 0.800052
"ENSRNOG00000011603.7" 1.26781 1.11454 1.41185 1.57576 1.07642 1.40583 0.337079 1.27965 0.628532 1.56735 0.914144 1.22786 1.77443 1.30843 1.30165 1.34342 2.07999 2.16342 1.64692 1.91808 2.04358 0.988442 1.94525 2.42002 1.8798 1.93388 1.75497 1.89908
"ENSRNOG00000011980.8" 1.58945 1.27887 0.952659 1.57479 1.59403 1.95603 0.174457 2.06151 2.07493 2.0474 1.71219 1.52264 1.93477 1.9758 2.05692 1.92448 1.74308 1.24029 1.4392 1.26188 1.30917 -4.59133 0.160715 3.88998 0.963238 0.9666 1.27523 0.838712
"ENSRNOG00000012136.7" 1.46784 1.81813 2.0135 1.87772 1.96569 2.44261 1.91997 1.95005 1.94212 1.97641 1.4981 1.7989 1.88443 2.26218 1.98936 2.14378 2.01103 1.40244 1.1728 1.7528 1.70433 1.16181 -1.56315 -2.99793 1.22404 1.51319 1.54227 1.15881
"ENSRNOG00000012360.6" 1.04148 0.988503 1.11527 1.21179 1.08909 1.27484 0.649559 0.945488 0.902212 0.931624 0.717814 0.580863 0.415762 1.15497 0.96694 0.905537 0.99383 1.1438 0.815796 0.901596 0.802891 1.27785 -0.699217 2.07303 0.881268 0.537995 0.856955 1.07771
"ENSRNOG00000012394.7" 1.9302 2.06848 1.88459 1.58369 1.88727 2.18529 1.99073 1.67461 2.09211 2.15856 2.05051 1.59411 1.9402 2.4683 2.52446 2.38755 1.92854 2.03495 2.01713 2.00842 1.89898 1.75049 2.70542 7.16721 2.15959 2.21986 2.0731 1.83411
"ENSRNOG00000012794.7" 0.753325 -0.12404 0.877674 0.21799 0.1188 -0.377793 0.19534 -0.360223 0.17421 0.453864 -0.00627037 1.02838 0.498753 0.719131 0.80095 0.500288 0.215262 0.918318 0.924336 0.906996 0.878161 2.08063 1.54865 -2.9131 1.05697 0.92187 0.599895 0.708622
"ENSRNOG00000012827.7" 1.21206 1.20721 1.4844 1.47506 1.67058 2.15126 1.48657 2.05755 1.8391 2.02054 1.87907 1.88301 1.47396 2.33518 2.16003 1.74856 1.88711 1.88228 1.93399 1.66341 1.90646 -10.5414 0.750533 -2.46153 2.29756 1.07077 2.18258 1.36834
"ENSRNOG00000013045.6" 1.36077 1.04511 1.20435 0.995718 1.12924 0.957959 1.38348 0.667408 1.07453 0.750494 1.1895 0.389295 0.9254 0.770581 0.70329 0.914617 1.45322 1.93902 1.8182 2.08182 1.98715 3.09069 2.06732 7.01448 2.01905 2.33443 1.9129 1.84581
"ENSRNOG00000013128.6" 1.70052 1.67202 1.81272 2.07815 2.16696 2.16941 1.95957 2.50184 2.4678 2.63583 3.21222 2.34879 2.4612 2.83775 2.66497 3.5811 3.04162 3.0296 3.05071 3.16559 3.29834 0.599966 2.28284 0.808801 3.03303 2.95419 3.16552 3.02576
"ENSRNOG00000013436.6" -0.070249 0.166406 0.0968053 0.301489 1.03894 1.22185 0.708002 1.50361 1.57573 2.02577 1.78755 2.06682 2.05214 2.08124 2.22586 1.97143 2.05417 1.96095 1.88695 1.79529 1.95941 1.61928 1.88779 2.18654 1.77508 1.57838 2.23799 2.15691
"ENSRNOG00000013581.3" 1.84915 1.99084 1.90258 1.82803 1.9737 1.93322 1.84804 2.18137 2.24522 2.19417 2.46276 2534 2.37351 2.9053 2.8986 2.9563 2.8726 2.53748 2.64402 2.41508 2.3193 1.09923 3.28885 1.96714 2.62382 2.68429 2.39141 2.32135
"ENSRNOG00000013802.8" 3.16585 2.81295 2.47332 2.97451 2.92529 2.82678 2.6186 2.66716 2.26929 2.86728 2.14097 2.45808 2.8484 3.35701 3.48891 2.97686 2.85392 2.76172 2.01539 2.6782 2.62193 2.49525 2.92017 7.29876 2.61115 2.67606 2.69169 2.78409
"ENSRNOG00000013919.6" 1.20604 1.18397 0.69444 0.934748 1.49087 1855 1.36672 1.25484 1.48712 1.65999 1.44651 1.97892 1.51917 1.55996 1.51576 1.16582 1.76894 1.55682 1.40135 1.59059 1.45354 2.20646 1.33265 2.15009 1.38778 1.52595 1.46532 1.06032
"ENSRNOG00000014197.6" 1.8326 1.91685 1.69984 1.87752 1.92753 2.18778 1.14266 2.04829 2.27199 2.38874 2.21418 2.40685 2.33255 1.27561 0.66182 1.78111 0.646029 1.27201 1.48688 1.09653 0.616501 -5.77716 0.185266 2.4367 1.31875 1.22235 1.06259 1.2283
"ENSRNOG00000014270.4" 2.13043 1.93631 2.17142 1.73056 1.73271 2.20849 1.97261 1.86924 1.36414 1.79335 1.51614 1.39374 0.99956 1.10068 1.01519 0.846567 1.17577 0.891188 1.0919 1.00923 1.53193 1.32242 1.33878 7.23473 1.01124 0.96812 1.28323 1.48874
"ENSRNOG00000014284.5" 0.734797 1.06184 1.59195 0.358771 0.056033 0.136241 0.556655 0.408303 0.485922 0.588404 0.633824 0.655131 -0.431787 -1.04252 -0.3868 0.254604 -1.06055 -0.126576 0.314569 0.379808 -0.692053 -0.494018 0.180635 -2.18135 -0.0443678 0.0235216 -0.501026 0.513477
"ENSRNOG00000014311.5" -0.14024 -0.221935 -0.028666 0.569718 -0.00890596 -0.416196 0.349359 -0.356139 -0.310759 -0.463595 0.160878 -0.631981 -0.489006 0.0538892 0.082097 0.270299 0.96295 0.3033 0.755115 0.550786 1.02117 0.639291 1.14546 1.95111 0.976638 0.527857 0.824445 0.723642
"ENSRNOG00000014475.4" 1.55946 1.69877 1.76235 1.29883 1.05941 1.38628 1.04452 1.13701 0.658832 1.03001 0.748904 0.258826 0.0803571 0.893431 0.171207 0.544407 -0.255203 -0.12444 0.015108 0.314923 0.596651 0.147218 -12.2676 -2.65649 -0.336677 0.512818 0.702075 0.943372
"ENSRNOG00000014493.6" 1.9313 1.88834 1.71906 1.86692 1.91421 1.91317 1.46825 1.84073 1.79665 1.81669 2.25499 1.78626 2.03065 1.84961 1.96613 2.33046 1.74227 2.18668 1997 2.18119 2.20311 2.49169 2.71337 7.30519 2.20724 2.0826 2.15583 2.00961
"ENSRNOG00000014635.8" 2.43607 2.3505 2.54051 1.55581 2.17753 2.42901 2.4042 2.14336 2.3436 2.44106 2.36733 2.35154 2.25091 2.16792 2.48116 2215 1.67609 1.80052 1.95122 1.45929 1.8699 1.71539 2.01911 7.49104 1.94966 1.94622 1.75962 1.55369
"ENSRNOG00000014675.2" 1.71631 1.81465 1.69236 1.85414 1.72651 2.30461 1.17568 1.58562 2.08749 2.03224 2.41698 2.30871 2.51251 3.41429 3.25237 3.07091 2.91198 2.91356 2.85482 2.74492 2.57449 3.03542 2.8867 8.04614 2.78742 2.54481 2.41897 2.44291
"ENSRNOG00000014828.5" 1.01656 0.787273 1.51834 1.05225 1266 1.65303 1.82163 1.85523 0.969592 1.34867 1.80952 1.20396 0.793441 1.27798 0.553838 0.839437 1.19264 1.1212 1.53181 1.51211 1.41858 1.26145 -11.1765 -3.53349 1.08677 1.17417 1.20366 1.47794
"ENSRNOG00000015117.5" 1.8483 1.64694 1.71835 2.35804 2.3084 2.43547 1.66588 2.03523 2.43196 2.57631 2.55427 2.71714 2.56381 2.52626 2.52519 2.72191 2.88195 2.8362 2.35056 2.41598 3.12081 -0.545688 2.69023 -2.92339 2.40581 2.1944 2.77586 2.35077
"ENSRNOG00000015142.4" 1.21368 0.872133 1.61173 0.969598 0.462713 1.12661 -0.703009 1.0907 0.625932 0.790624 0.826364 0.340733 0.574859 0.757031 0.89797 0.541237 0.91918 1.27873 1.0219 1.24934 1.25887 -10.5604 0.327821 -2.70676 0.723775 0.785439 1.17436 0.979792
"ENSRNOG00000015255.6" 0.635166 1.09467 0.960959 1.23027 0.831073 1.59706 0.60128 1.09024 0.787662 1.31644 -0.570947 0.256745 0.389404 -0.644887 -1.21314 -0.77266 -0.342358 -0.209389 -0.789478 -0.546111 -0.0696438 0.572373 -12.1533 -3.27651 -0.288691 0.247212 0.063807 -0.0788222
"ENSRNOG00000015271.7" 0.34225 -0.0864621 -0.420396 0.947378 0.22373 0.646939 0.334785 0.600073 0.126738 0.214864 0.301494 -0.701341 -0.329095 0.23911 0.495603 0.404036 0.484115 0.689228 0.704947 0.670936 0.742831 0.659101 0.905933 1.90036 0.766806 0.667169 0.933665 0.842992
"ENSRNOG00000015488.7" 3.45224 3.30972 3.1981 3.16098 3.53076 3.61891 3.31948 3.4722 3.89426 3.73517 3.58889 3.76377 3.73657 3.9276 4.1647 3775 3.1758 3.52078 3.25142 3.47916 3.52366 3.87992 4.2406 7.27741 3.33201 3.22192 3.22409 3.27264
"ENSRNOG00000015718.5" -0.604849 -0.914111 -1.37528 -0.514172 -0.533857 -0.153083 -7.3498 -1.37349 0.346189 -0.0866821 0.417644 -0.380773 0.203298 0.915931 0.148214 0.820207 0.559821 0.811228 1.50097 1.01426 1.10617 -6.61361 0.889786 1.94846 1.34223 1.24974 1.10228 1.17295
"ENSRNOG00000015762.6" 1.2063 1.13676 1.24927 1.01618 1.49932 1.40316 1.76073 1.41854 1.97302 1.67342 2.00881 2.47602 2.70518 2.41738 2.21105 2.22312 2.11051 2.06415 2.29378 2.0739 1.97781 3.05224 2.69214 -2.74887 2.17244 2.07997 1.74751 1.799

@abhisheksinghnl
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Hi,

Thank you.

Possibly the last one, I have a lot of NaNs, is it wise to remove them?

Best

@eturro
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eturro commented Sep 26, 2016

Where are the NaNs?

On 26 Sep 2016, at 15:17, abhisheksinghnl notifications@github.com wrote:

Hi,

Thank you.

Possibly the last one, I have a lot of NaNs, is it wise to remove them?

Best

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Hi,

Sorry, it is NA not NAN.

Shall remove the lines carrying NA or replace them with 0? what is best way
to deal with these?

Best regards
Abhishek

On Mon, Sep 26, 2016 at 4:27 PM, Ernest Turro notifications@github.com
wrote:

Where are the NaNs?

On 26 Sep 2016, at 15:17, abhisheksinghnl notifications@github.com
wrote:

Hi,

Thank you.

Possibly the last one, I have a lot of NaNs, is it wise to remove them?

Best

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eturro commented Sep 26, 2016

Which column of which file do you see NAs in?

On 26 Sep 2016, at 15:34, abhisheksinghnl notifications@github.com wrote:

Hi,

Sorry, it is NA not NAN.

Shall remove the lines carrying NA or replace them with 0? what is best way
to deal with these?

Best regards
Abhishek

On Mon, Sep 26, 2016 at 4:27 PM, Ernest Turro notifications@github.com
wrote:

Where are the NaNs?

On 26 Sep 2016, at 15:17, abhisheksinghnl notifications@github.com
wrote:

Hi,

Thank you.

Possibly the last one, I have a lot of NaNs, is it wise to remove them?

Best

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here it is

"feature_id" "mu_E18_1,namesorted,bam,hits,gene" "mu_E18_2,namesorted,bam,hits,gene" "mu_E18_3,namesorted,bam,hits,gene" "mu_E18_4,namesorted,bam,hits,gene" "mu_P1_1,namesorted,bam,hits,gene" "mu_P1_2,namesorted,bam,hits,gene" "mu_P1_3,namesorted,bam,hits,gene" "mu_P3_1,namesorted,bam,hits,gene" "mu_P3_2,namesorted,bam,hits,gene" "mu_P3_3,namesorted,bam,hits,gene" "mu_P10_1,namesorted,bam,hits,gene" "mu_P10_2,namesorted,bam,hits,gene" "mu_P10_3,namesorted,bam,hits,gene" "mu_Mo3_1,namesorted,bam,hits,gene" "mu_Mo3_2,namesorted,bam,hits,gene" "mu_Mo3_3,namesorted,bam,hits,gene" "mu_Mo3_4,namesorted,bam,hits,gene" "mu_Mo12_1,namesort,bam,hits,gene" "mu_Mo12_2,namesort,bam,hits,gene" "mu_Mo12_3,namesort,bam,hits,gene" "mu_Mo12_4,namesort,bam,hits,gene" "mu_Mo24_1,namesort,bam,hits,gene" "mu_Mo24_2,namesort,bam,hits,gene" "mu_Mo24_3,namesort,bam,hits,gene" "mu_Mo24_4,namesort,bam,hits,gene" "mu_Mo24_5,namesort,bam,hits,gene" "mu_Mo24_6,namesort,bam,hits,gene" "mu_Mo24_7,namesort,bam,hits,gene" "postprob_model0" "postprob_model1" "postprob_model2" "postprob_model3" "postprob_model4" "postprob_model5" "postprob_model6" "postprob_model7"

"ENSRNOG00000000044,6" 1,93077 1,77034 1,94492 2,01215 2,07374 2,27246 2,10575 2,20234 2,41065 2,22659 2,37298 2,2594 2,47746 2,67266 2,6812 2726 2,34917 2,43676 2,2224 2,29195 2,35387 1,93058 2,06998 7,05513 2,37321 2,24386 2,29025 2,29686 0 NA NA 0 0 NA NA NA
"ENSRNOG00000000066,5" 1,92875 1,81539 2,08403 1,87709 2,1959 2,14811 1,90647 2,21202 2,37195 2,21731 2,45489 1,64541 2,24419 2,10418 2,13605 2,2231 1,17135 1,46443 1,73503 1,51585 1,08541 1,50488 1,05449 -2,73053 1,5211 1,36829 1,52562 1,42293 0 NA NA 0 0 0 0 0
"ENSRNOG00000000098,7" 1,23244 1,01857 1,35909 1,41719 1,71721 1,84907 1,40537 2,08355 1,6536 2,06811 1,75018 1,94563 2,55977 2,33215 1,96623 2,21867 2,33136 1,86095 2,04603 2,19401 2,09354 1,00136 1,81151 -2,88187 1,73583 1,92559 2,05915 2,16223 0 NA NA NA 0 0 0 0

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eturro commented Sep 26, 2016

Hmmm, did you use version 1.0.9 of mmdiff?

Would you mind printing out the posterior probabilities and the Bayes factors recorded in the seven comparison mmdiff files for one of the features, e.g. ENSRNOG00000000098.7?

Thanks
Ernest

On 26 Sep 2016, at 15:39, abhisheksinghnl notifications@github.com wrote:

here it is

"feature_id" "mu_E18_1,namesorted,bam,hits,gene" "mu_E18_2,namesorted,bam,hits,gene" "mu_E18_3,namesorted,bam,hits,gene" "mu_E18_4,namesorted,bam,hits,gene" "mu_P1_1,namesorted,bam,hits,gene" "mu_P1_2,namesorted,bam,hits,gene" "mu_P1_3,namesorted,bam,hits,gene" "mu_P3_1,namesorted,bam,hits,gene" "mu_P3_2,namesorted,bam,hits,gene" "mu_P3_3,namesorted,bam,hits,gene" "mu_P10_1,namesorted,bam,hits,gene" "mu_P10_2,namesorted,bam,hits,gene" "mu_P10_3,namesorted,bam,hits,gene" "mu_Mo3_1,namesorted,bam,hits,gene" "mu_Mo3_2,namesorted,bam,hits,gene" "mu_Mo3_3,namesorted,bam,hits,gene" "mu_Mo3_4,namesorted,bam,hits,gene" "mu_Mo12_1,namesort,bam,hits,gene" "mu_Mo12_2,namesort,bam,hits,gene" "mu_Mo12_3,namesort,bam,hits,gene" "mu_Mo12_4,namesort,bam,hits,gene" "mu_Mo24_1,namesort,bam,hits,gene" "mu_Mo24_2,namesort,bam,hits,gene" "mu_Mo24_3,namesort,bam,hits,gene" "mu_Mo24_4,namesort,bam,hits,gene" "mu_Mo24_5,namesort,bam,hits,gene" "mu_Mo24_6,namesort,bam,hits,gene" "mu_Mo24_7,namesort,bam,hits,gene" "postprob_model0" "postprob_model1" "postprob_model2" "postprob_model3" "postprob_model4" "postprob_model5" "postprob_model6" "postprob_model7"

"ENSRNOG00000000044,6" 1,93077 1,77034 1,94492 2,01215 2,07374 2,27246 2,10575 2,20234 2,41065 2,22659 2,37298 2,2594 2,47746 2,67266 2,6812 2726 2,34917 2,43676 2,2224 2,29195 2,35387 1,93058 2,06998 7,05513 2,37321 2,24386 2,29025 2,29686 0 NA NA 0 0 NA NA NA
"ENSRNOG00000000066,5" 1,92875 1,81539 2,08403 1,87709 2,1959 2,14811 1,90647 2,21202 2,37195 2,21731 2,45489 1,64541 2,24419 2,10418 2,13605 2,2231 1,17135 1,46443 1,73503 1,51585 1,08541 1,50488 1,05449 -2,73053 1,5211 1,36829 1,52562 1,42293 0 NA NA 0 0 0 0 0
"ENSRNOG00000000098,7" 1,23244 1,01857 1,35909 1,41719 1,71721 1,84907 1,40537 2,08355 1,6536 2,06811 1,75018 1,94563 2,55977 2,33215 1,96623 2,21867 2,33136 1,86095 2,04603 2,19401 2,09354 1,00136 1,81151 -2,88187 1,73583 1,92559 2,05915 2,16223 0 NA NA NA 0 0 0 0

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The version of mmdiff is mmdiff-1.0.8

feature_id bayes_factor posterior_probability alpha0 beta0_0 beta0_1 beta0_2 beta0_3 beta0_4 beta0_5 beta0_6 alpha1 beta1_0 beta1_1 beta1_2 beta1_3 beta1_4 beta1_5 beta1_6 eta1_0 mu_E18_1.namesorted.bam.hits.gene mu_E18_2.namesorted.bam.hits.gene mu_E18_3.namesorted.bam.hits.gene mu_E18_4.namesorted.bam.hits.gene mu_P1_1.namesorted.bam.hits.gene mu_P1_2.namesorted.bam.hits.gene mu_P1_3.namesorted.bam.hits.gene mu_P3_1.namesorted.bam.hits.gene mu_P3_2.namesorted.bam.hits.gene mu_P3_3.namesorted.bam.hits.gene mu_P10_1.namesorted.bam.hits.gene mu_P10_2.namesorted.bam.hits.gene mu_P10_3.namesorted.bam.hits.gene mu_Mo3_1.namesorted.bam.hits.gene mu_Mo3_2.namesorted.bam.hits.gene mu_Mo3_3.namesorted.bam.hits.gene mu_Mo3_4.namesorted.bam.hits.gene mu_Mo12_1.namesort.bam.hits.gene mu_Mo12_2.namesort.bam.hits.gene mu_Mo12_3.namesort.bam.hits.gene mu_Mo12_4.namesort.bam.hits.gene mu_Mo24_1.namesort.bam.hits.gene mu_Mo24_2.namesort.bam.hits.gene mu_Mo24_3.namesort.bam.hits.gene mu_Mo24_4.namesort.bam.hits.gene mu_Mo24_5.namesort.bam.hits.gene mu_Mo24_6.namesort.bam.hits.gene mu_Mo24_7.namesort.bam.hits.gene sd_E18_1.namesorted.bam.hits.gene sd_E18_2.namesorted.bam.hits.gene sd_E18_3.namesorted.bam.hits.gene sd_E18_4.namesorted.bam.hits.gene sd_P1_1.namesorted.bam.hits.gene sd_P1_2.namesorted.bam.hits.gene sd_P1_3.namesorted.bam.hits.gene sd_P3_1.namesorted.bam.hits.gene sd_P3_2.namesorted.bam.hits.gene sd_P3_3.namesorted.bam.hits.gene sd_P10_1.namesorted.bam.hits.gene sd_P10_2.namesorted.bam.hits.gene sd_P10_3.namesorted.bam.hits.gene sd_Mo3_1.namesorted.bam.hits.gene sd_Mo3_2.namesorted.bam.hits.gene sd_Mo3_3.namesorted.bam.hits.gene sd_Mo3_4.namesorted.bam.hits.gene sd_Mo12_1.namesort.bam.hits.gene sd_Mo12_2.namesort.bam.hits.gene sd_Mo12_3.namesort.bam.hits.gene sd_Mo12_4.namesort.bam.hits.gene sd_Mo24_1.namesort.bam.hits.gene sd_Mo24_2.namesort.bam.hits.gene sd_Mo24_3.namesort.bam.hits.gene sd_Mo24_4.namesort.bam.hits.gene sd_Mo24_5.namesort.bam.hits.gene sd_Mo24_6.namesort.bam.hits.gene sd_Mo24_7.namesort.bam.hits.gene

ENSRNOG00000000098.7 0.0190623 0.00211356 1.82557 -0.604319 -0.175977 0.0598454 0.22367 0.338942 0.176893 0.0316759 1.4831 -0.502818 -0.0845974 0.169414 0.315968 0.435606 0.265885 0.441127 -0.414926 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

@eturro
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eturro commented Sep 26, 2016

Could you print out this line across all seven files please?

This one looks fine (Bayes factor of 0.0190623 and posterior probability of 0.00211356) but I think some of the other files may have NA or NaN due to an issue that I resolved in version 1.0.9

On 26 Sep 2016, at 15:52, abhisheksinghnl notifications@github.com wrote:

The version of mmdiff is mmdiff-1.0.8

feature_id bayes_factor posterior_probability alpha0 beta0_0 beta0_1 beta0_2 beta0_3 beta0_4 beta0_5 beta0_6 alpha1 beta1_0 beta1_1 beta1_2 beta1_3 beta1_4 beta1_5 beta1_6 eta1_0 mu_E18_1.namesorted.bam.hits.gene mu_E18_2.namesorted.bam.hits.gene mu_E18_3.namesorted.bam.hits.gene mu_E18_4.namesorted.bam.hits.gene mu_P1_1.namesorted.bam.hits.gene mu_P1_2.namesorted.bam.hits.gene mu_P1_3.namesorted.bam.hits.gene mu_P3_1.namesorted.bam.hits.gene mu_P3_2.namesorted.bam.hits.gene mu_P3_3.namesorted.bam.hits.gene mu_P10_1.namesorted.bam.hits.gene mu_P10_2.namesorted.bam.hits.gene mu_P10_3.namesorted.bam.hits.gene mu_Mo3_1.namesorted.bam.hits.gene mu_Mo3_2.namesorted.bam.hits.gene mu_Mo3_3.namesorted.bam.hits.gene mu_Mo3_4.namesorted.bam.hits.gene mu_Mo12_1.namesort.bam.hits.gene mu_Mo12_2.namesort.bam.hits.gene mu_Mo12_3.namesort.bam.hits.gene mu_Mo12_4.namesort.bam.hits.gene mu_Mo24_1.namesort.bam.hits.gene mu_Mo24_2.namesort.bam.hits.gene mu_Mo24_3.namesort.bam.hits.gene mu_Mo24_4.namesort.bam.hits.gene mu_Mo24_5.namesort.bam.hits.gene mu_Mo24_6.namesort.bam.hits.gene mu_Mo24_7.namesort.bam.hits.gene sd_E18_1.namesorted.bam.hits.gene sd_E18_2.namesorted.bam.hits.gene sd_E18_3.namesorted.bam.hits.gene sd_E18_4.namesorted.bam.hits.gene sd_P1_1.namesorted.bam.hits.gene sd_P1_2.namesorted.bam.hits.gene sd_P1_3.namesorted.bam.hits.gene sd_P3_1.namesorted.bam.hits.gene sd_P3_2.namesorted.bam.hits.gene sd_P3_3.namesorted.bam.hits.gene sd_P10_1.namesorted.bam.hits.gene sd_P10_2.namesorted.bam.hits.gene sd_P10_3.namesorted.bam.hits.gene sd_Mo3_1.namesorted.bam.hits.gene sd_Mo3_2.namesorted.bam.hits.gene sd_Mo3_3.namesorted.bam.hits.gene sd_Mo3_4.namesorted.bam.hits.gene sd_Mo12_1.namesort.bam.hits.gene sd_Mo12_2.namesort.bam.hits.gene sd_Mo12_3.namesort.bam.hits.gene sd_Mo12_4.namesort.bam.hits.gene sd_Mo24_1.namesort.bam.hits.gene sd_Mo24_2.namesort.bam.hits.gene sd_Mo24_3.namesort.bam.hits.gene sd_Mo24_4.namesort.bam.hits.gene sd_Mo24_5.namesort.bam.hits.gene sd_Mo24_6.namesort.bam.hits.gene sd_Mo24_7.namesort.bam.hits.gene

ENSRNOG00000000098.7 0.0190623 0.00211356 1.82557 -0.604319 -0.175977 0.0598454 0.22367 0.338942 0.176893 0.0316759 1.4831 -0.502818 -0.0845974 0.169414 0.315968 0.435606 0.265885 0.441127 -0.414926 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

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@abhisheksinghnl
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Here they are:

feature_id bayes_factor posterior_probability alpha0 beta0_0 beta0_1 beta0_2 beta0_3 beta0_4 beta0_5 beta0_6 alpha1 beta1_0 beta1_1 beta1_2 beta1_3 beta1_4 beta1_5 beta1_6 eta1_0 mu_E18_1.namesorted.bam.hits.gene mu_E18_2.namesorted.bam.hits.gene mu_E18_3.namesorted.bam.hits.gene mu_E18_4.namesorted.bam.hits.gene mu_P1_1.namesorted.bam.hits.gene mu_P1_2.namesorted.bam.hits.gene mu_P1_3.namesorted.bam.hits.gene mu_P3_1.namesorted.bam.hits.gene mu_P3_2.namesorted.bam.hits.gene mu_P3_3.namesorted.bam.hits.gene mu_P10_1.namesorted.bam.hits.gene mu_P10_2.namesorted.bam.hits.gene mu_P10_3.namesorted.bam.hits.gene mu_Mo3_1.namesorted.bam.hits.gene mu_Mo3_2.namesorted.bam.hits.gene mu_Mo3_3.namesorted.bam.hits.gene mu_Mo3_4.namesorted.bam.hits.gene mu_Mo12_1.namesort.bam.hits.gene mu_Mo12_2.namesort.bam.hits.gene mu_Mo12_3.namesort.bam.hits.gene mu_Mo12_4.namesort.bam.hits.gene mu_Mo24_1.namesort.bam.hits.gene mu_Mo24_2.namesort.bam.hits.gene mu_Mo24_3.namesort.bam.hits.gene mu_Mo24_4.namesort.bam.hits.gene mu_Mo24_5.namesort.bam.hits.gene mu_Mo24_6.namesort.bam.hits.gene mu_Mo24_7.namesort.bam.hits.gene sd_E18_1.namesorted.bam.hits.gene sd_E18_2.namesorted.bam.hits.gene sd_E18_3.namesorted.bam.hits.gene sd_E18_4.namesorted.bam.hits.gene sd_P1_1.namesorted.bam.hits.gene sd_P1_2.namesorted.bam.hits.gene sd_P1_3.namesorted.bam.hits.gene sd_P3_1.namesorted.bam.hits.gene sd_P3_2.namesorted.bam.hits.gene sd_P3_3.namesorted.bam.hits.gene sd_P10_1.namesorted.bam.hits.gene sd_P10_2.namesorted.bam.hits.gene sd_P10_3.namesorted.bam.hits.gene sd_Mo3_1.namesorted.bam.hits.gene sd_Mo3_2.namesorted.bam.hits.gene sd_Mo3_3.namesorted.bam.hits.gene sd_Mo3_4.namesorted.bam.hits.gene sd_Mo12_1.namesort.bam.hits.gene sd_Mo12_2.namesort.bam.hits.gene sd_Mo12_3.namesort.bam.hits.gene sd_Mo12_4.namesort.bam.hits.gene sd_Mo24_1.namesort.bam.hits.gene sd_Mo24_2.namesort.bam.hits.gene sd_Mo24_3.namesort.bam.hits.gene sd_Mo24_4.namesort.bam.hits.gene sd_Mo24_5.namesort.bam.hits.gene sd_Mo24_6.namesort.bam.hits.gene sd_Mo24_7.namesort.bam.hits.gene

ENSRNOG00000000098.7 inf 1 -nan -0.435103 -0.0140217 0.226919 0.385137 0.507219 0.349306 0.186145 1.87446 -0.491195 -0.294448 -0.0502627 0.109003 0.224025 0.0621883 -0.0840703 -0.223738 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 inf 1 -nan -0.438551 -0.014951 0.235706 0.384479 0.505696 0.35142 0.181437 1.89396 -0.622727 -0.206974 0.0436585 0.201801 0.318719 0.156792 0.00888626 0.00289205 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 inf 1 -nan -0.446658 -0.0015702 0.235258 0.389591 0.502541 0.32965 0.202072 1.99038 -0.702985 -0.282921 -0.0720392 0.120476 0.239042 0.0766737 -0.0709585 0.0332761 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 0 0 1.78696 -0.518377 -0.0942221 0.149615 0.308135 0.423671 0.26336 0.115039 -nan -0.555334 -0.135602 0.11226 0.303931 0.386602 0.222534 0.0869579 -nan 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

@eturro
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eturro commented Sep 26, 2016

Yes, so you can see that for this feature the Bayes factor is infinite in several of the comparisons.

In these cases, you have very strong evidence against the baseline model but it's not clear which of the alternative models is a better fit because each one is so overwhelmingly better fitting than the baseline model that gamma was estimated as being 1 (and the Bayes factor as infinite) in several comparison.

As a quick workaround you could manipulate the Bayes factors that are infinite and change them to a very high value. Similarly increase slightly the ones that are zero to just above zero.

In mmseq.R, in this loop:

 for(j in 1:length(files)) {
    bf[,j+1] <- read.table(files[j],header=1)$bayes_factor
  }

You could add:

    bf[,j+1][is.infinite(bf[,j+1])]=large_val
    bf[,j+1][bf[,j+1]==0]=small_val

where large_val is something slightly larger than the largest Bayes factor you've observed and small_val (near zero) is something slightly closer to zero than any other Bayes factor you've observed.

It's a bit of a hack but a fairly principled one and it will allow you to include these features in the ranking.

Note that if your prior is the same across the different models, and you have a mixture of infinite and zero Bayes factors, you'll essentially end up with posterior probability = 1 / number of models with an infinite Bayes factor, which could be quite low in your situation, given you are comparing seven models.

best wishes
Ernest

On 26 Sep 2016, at 16:07, abhisheksinghnl notifications@github.com wrote:

Here they are:

feature_id bayes_factor posterior_probability alpha0 beta0_0 beta0_1 beta0_2 beta0_3 beta0_4 beta0_5 beta0_6 alpha1 beta1_0 beta1_1 beta1_2 beta1_3 beta1_4 beta1_5 beta1_6 eta1_0 mu_E18_1.namesorted.bam.hits.gene mu_E18_2.namesorted.bam.hits.gene mu_E18_3.namesorted.bam.hits.gene mu_E18_4.namesorted.bam.hits.gene mu_P1_1.namesorted.bam.hits.gene mu_P1_2.namesorted.bam.hits.gene mu_P1_3.namesorted.bam.hits.gene mu_P3_1.namesorted.bam.hits.gene mu_P3_2.namesorted.bam.hits.gene mu_P3_3.namesorted.bam.hits.gene mu_P10_1.namesorted.bam.hits.gene mu_P10_2.namesorted.bam.hits.gene mu_P10_3.namesorted.bam.hits.gene mu_Mo3_1.namesorted.bam.hits.gene mu_Mo3_2.namesorted.bam.hits.gene mu_Mo3_3.namesorted.bam.hits.gene mu_Mo3_4.namesorted.bam.hits.gene mu_Mo12_1.namesort.bam.hits.gene mu_Mo12_2.namesort.bam.hits.gene mu_Mo12_3.namesort.bam.hits.gene mu_Mo12_4.namesort.bam.hits.gene mu_Mo24_1.namesort.bam.hits.gene mu_Mo24_2.namesort.bam.hits.gene mu_Mo24_3.namesort.bam.hits.gene mu_Mo24_4.namesort.bam.hits.gene mu_Mo24_5.namesort.bam.hits.gene mu_Mo24_6.namesort.bam.hits.gene mu_Mo24_7.namesort.bam.hits.gene sd_E18_1.namesorted.bam.hits.gene sd_E18_2.namesorted.bam.hits.gene sd_E18_3.namesorted.bam.hits.gene sd_E18_4.namesorted.bam.hits.gene sd_P1_1.namesorted.bam.hits.gene sd_P1_2.namesorted.bam.hits.gene sd_P1_3.namesorted.bam.hits.gene sd_P3_1.namesorted.bam.hits.gene sd_P3_2.namesorted.bam.hits.gene sd_P3_3.namesorted.bam.hits.gene sd_P10_1.namesorted.bam.hits.gene sd_P10_2.namesorted.bam.hits.gene sd_P10_3.namesorted.bam.hits.gene sd_Mo3_1.namesorted.bam.hits.gene sd_Mo3_2.namesorted.bam.hits.gene sd_Mo3_3.namesorted.bam.hits.gene sd_Mo3_4.namesorted.bam.hits.gene sd_Mo12_1.namesort.bam.hits.gene sd_Mo12_2.namesort.bam.hits.gene sd_Mo12_3.namesort.bam.hits.gene sd_Mo12_4.namesort.bam.hits.gene sd_Mo24_1.namesort.bam.hits.gene sd_Mo24_2.namesort.bam.hits.gene sd_Mo24_3.namesort.bam.hits.gene sd_Mo24_4.namesort.bam.hits.gene sd_Mo24_5.namesort.bam.hits.gene sd_Mo24_6.namesort.bam.hits.gene sd_Mo24_7.namesort.bam.hits.gene

ENSRNOG00000000098.7 inf 1 -nan -0.435103 -0.0140217 0.226919 0.385137 0.507219 0.349306 0.186145 1.87446 -0.491195 -0.294448 -0.0502627 0.109003 0.224025 0.0621883 -0.0840703 -0.223738 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 inf 1 -nan -0.438551 -0.014951 0.235706 0.384479 0.505696 0.35142 0.181437 1.89396 -0.622727 -0.206974 0.0436585 0.201801 0.318719 0.156792 0.00888626 0.00289205 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 inf 1 -nan -0.446658 -0.0015702 0.235258 0.389591 0.502541 0.32965 0.202072 1.99038 -0.702985 -0.282921 -0.0720392 0.120476 0.239042 0.0766737 -0.0709585 0.0332761 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

ENSRNOG00000000098.7 0 0 1.78696 -0.518377 -0.0942221 0.149615 0.308135 0.423671 0.26336 0.115039 -nan -0.555334 -0.135602 0.11226 0.303931 0.386602 0.222534 0.0869579 -nan 1.23244 1.01857 1.35909 1.41719 1.71721 1.84907 1.40537 2.08355 1.6536 2.06811 1.75018 1.94563 2.55977 2.33215 1.96623 2.21867 2.33136 1.86095 2.04603 2.19401 2.09354 1.00136 1.81151 -2.88187 1.73583 1.92559 2.05915 2.16223 0.167869 0.165434 0.16887 0.108137 0.0938489 0.118504 0.214196 0.105806 0.108486 0.101371 0.110449 0.129985 0.0992743 0.101388 0.0961584 0.100015 0.080088 0.0841759 0.0798832 0.0635577 0.0931624 0.438508 0.192649 9.84077 0.108151 0.0894878 0.0723886 0.101675

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@eturro @abhisheksinghnl