Error from 4Cker tranAnalysis

[amarsh33]

Hello,

I ran 2 different transAnalyses recently for 2 different viewpoints. The one viewpoint worked okay but did give me the following errors (along with the normal output):

Usp5_trans_results=transAnalysis(Usp5_obj,k=20)
[1] "Building adaptive windows..."
[1] "Normalizing counts..."
[1] "Generating synthetic samples...."
[1] "Parameter estimation....."

Iter: 1 fn: 3701131.7085 Pars: 0.33333 0.33333 0.33333 0.50000 0.25000 0.25000 0.25000 0.50000 0.25000 0.25000 0.25000 0.50000 1.35778 0.11122 2.17244 0.01167 2.71555 0.02963
solnp--> Solution not reliable....Problem Inverting Hessian.
[1] "Warning: only 1 iteration. Using starting parameters"
[1] "BED file of highest interacting domains for trans chromosomes are saved in /Volumes/hd2/4C_seq/analysis/4Cker/Usp5_results/"
Warning message:
In p0 * vscale[(neq + 2):(nc + np + 1)] :
longer object length is not a multiple of shorter object length

However, my analysis from the other viewpoint did not complete and gave me some additional errors:

Pxmp2_trans_results=transAnalysis(Pxmp2_obj,k=20)
[1] "Building adaptive windows..."
[1] "Normalizing counts..."
[1] "Generating synthetic samples...."
[1] "Parameter estimation....."

Iter: 1 fn: 6322212.6504 Pars: 0.333333 0.333333 0.333333 0.500000 0.250000 0.250000 0.250000 0.500000 0.250000 0.250000 0.250000 0.500000 1.211190 0.063576 1.937904 0.007503 2.422380 0.038934
solnp--> Solution not reliable....Problem Inverting Hessian.
[1] "Warning: only 1 iteration. Using starting parameters"
Error in state[et[case]] <- which.max(delta[et[case], ]) :
replacement has length zero
In addition: Warning message:
In p0 * vscale[(neq + 2):(nc + np + 1)] :
longer object length is not a multiple of shorter object length

I was just wondering what was causing this error that is causing the job to stop running, and what I should be doing to have more iterations through the data so I don't get the warning messages any more either.

[rr1859]

Hi,

What primary enzyme are you using for the 4C-Seq experiment? In our experience when you use 4bp cutters, you need very high sequencing depth to call trans interactions

[amarsh33]

Hello, I used HindIII as my primary enzyme. The depth of sequencing for my replicates did differ though, which may have caused the error. Thanks. On Aug 20, 2017, at 10:10 PM, Ramya Raviram <notifications@github.com<mailto:notifications@github.com>> wrote: Hi, What primary enzyme are you using for the 4C-Seq experiment? In our experience when you use 4bp cutters, you need very high sequencing depth to call trans interactions — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#37 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/APLITLkifi6GCUw9Qa8FTD2NScBjOKf9ks5saOcYgaJpZM4O2zs2>.