IsomirDataSeqFromFiles error #2

hmkim · 2016-04-28T04:28:04Z

> obj <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
Error in initialize(value, ...) : 
  cannot use object of class “SummarizedExperiment0” in new():  class “IsomirDataSeq” does not extend that class

Hi, Ipantano

Would you give me any suggestion about this error ?

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lpantano · 2016-04-28T12:06:51Z

hum, can you send me the sessionInfo() output? I think is a problem of version. Did you install the package recently?

sent not from my computer

On Apr 28, 2016, at 00:28, Hyunmin notifications@github.com wrote:

obj <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
Error in initialize(value, ...) :
cannot use object of class “SummarizedExperiment0” in new(): class “IsomirDataSeq” does not extend that class
Hi, Ipantano

Would you give me any suggestion about this error ?

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lpantano · 2016-04-28T14:06:10Z

can you check to install again this package from github origin/master. I think is a problem with summarixedexperiment object and maybe I fixed it.

thanks

hmkim · 2016-04-30T18:12:52Z

Ok. I'll try to run again and report it.

Thanks.

hmkim · 2016-05-25T07:08:34Z

Sorry for delaying of my reply.

I solve the before problem.

I have another issue about this function in Isomir.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = TRUE)

> design
     type batch phenotype
PK_1   PK  None        PK
PI_1   PI  None        PI
PI_2   PI  None        PI
SI_1   SI  None        SI
SI_2   SI  None        SI
SK_1   SK  None        SK

> files[rownames(design)]
                                                               PK_1 
"/Users/brandon/Downloads/work/upload/PK_1/PK_1-novel-ready.counts" 
                                                               PI_1 
"/Users/brandon/Downloads/work/upload/PI_1/PI_1-novel-ready.counts" 
                                                               PI_2 
"/Users/brandon/Downloads/work/upload/PI_2/PI_2-novel-ready.counts" 
                                                               SI_1 
"/Users/brandon/Downloads/work/upload/SI_1/SI_1-novel-ready.counts" 
                                                               SI_2 
"/Users/brandon/Downloads/work/upload/SI_2/SI_2-novel-ready.counts" 
                                                               SK_1 
"/Users/brandon/Downloads/work/upload/SK_1/SK_1-novel-ready.counts"

Can you check this error?

lpantano · 2016-05-25T12:19:11Z

Hi,

what is the error you are getting?

sent not from my computer

On May 25, 2016, at 03:08, Hyunmin notifications@github.com wrote:

Sorry for delaying my reply.

I solve the before problem.

I have another issue about this function in Isomir.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = TRUE)

design
type batch phenotype
PK_1 PK None PK
PI_1 PI None PI
PI_2 PI None PI
SI_1 SI None SI
SI_2 SI None SI
SK_1 SK None SK
files[rownames(design)]
PK_1
"/Users/brandon/Downloads/work/upload/PK_1/PK_1-novel-ready.counts"
PI_1
"/Users/brandon/Downloads/work/upload/PI_1/PI_1-novel-ready.counts"
PI_2
"/Users/brandon/Downloads/work/upload/PI_2/PI_2-novel-ready.counts"
SI_1
"/Users/brandon/Downloads/work/upload/SI_1/SI_1-novel-ready.counts"
SI_2
"/Users/brandon/Downloads/work/upload/SI_2/SI_2-novel-ready.counts"
SK_1
"/Users/brandon/Downloads/work/upload/SK_1/SK_1-novel-ready.counts"
Can you check this error?

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hmkim · 2016-05-26T04:52:24Z

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
Error in if (row["subs"] == "0") return(c(.seq, row["subs"])) else if (sum(tab.fil$subs == :
missing value where TRUE/FALSE needed

I think this error come up with my data. Can you check this ?

lpantano · 2016-05-26T14:50:02Z

Can you check this code to isolate what file is giving the error:

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)

Also, can you paste the few lines of some of the file is reading, just in case there is something obvious.

hmkim · 2016-05-30T02:28:14Z

> obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)
Error: object 'False' not found

novel miRNA by mirdeep2

total miRNA expression

files = mirdeep2_files

names(files) = sapply(files, function(x){
  gsub("-novel-ready.counts", "", basename(x))
})

#obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)

If you want to any data related to this problem, please tell me about that.

Thanks!

lpantano · 2016-05-30T13:45:14Z

sorry, it should be FALSE

let me know the output. Then if we get one file is failing maybe you can sending me file to my email.

thanks

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On May 29, 2016, at 22:28, Hyunmin notifications@github.com wrote:

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)
Error: object 'False' not found

novel miRNA by mirdeep2

total miRNA expression

files = mirdeep2_files

names(files) = sapply(files, function(x){
gsub("-novel-ready.counts", "", basename(x))
})

#obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T)
obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design)], design = design , header = T, quiet=False)
If you want to any data related to this problem, please tell me about that.

Thanks!

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hmkim · 2016-05-31T06:51:42Z

I might find the cause of problem.

If some samples don't have the novel miRNA, it is badly for IsomirDataSeqFromFiles.

[design2] have only SI_1, SI_2 and SK_1 sample.

obj_mirdeep <- IsomirDataSeqFromFiles(files = files[rownames(design2)], design = design2 , header = T)

simonas-j · 2016-10-20T07:51:28Z

Hi Ipantano,

I'm getting the same error and I have no clue what could cause it. See the code below:

head(metafile, n=2)
Condition
D1416 GIST
D1417 GISTaj

head(files.list, n=2)
D1416
"/home/simonas/Results/isomir_D1416.mirna"
D1417
"/home/simonas/Results/isomir_D1417.mirna"

ids <- IsomirDataSeqFromFiles(files.list, design=metafile, header = TRUE, quiet= FALSE)
reading file: /home/simonas/Results/isomir_D1416.mirna
Error in if (row["subs"] == "0") return(c(.seq, row["subs"])) else if (sum(tab.fil$subs == :
missing value where TRUE/FALSE needed
In addition: Warning message:
In .put_header(table) : NAs introduced by coercion

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] stringr_1.1.0 isomiRs_1.1.5 SummarizedExperiment_1.2.3 Biobase_2.32.0 GenomicRanges_1.24.3 GenomeInfoDb_1.8.7
[7] IRanges_2.6.1 S4Vectors_0.10.3 BiocGenerics_0.18.0 DiscriMiner_0.1-29

loaded via a namespace (and not attached):
[1] genefilter_1.54.2 gtools_3.5.0 locfit_1.5-9.1 splines_3.3.1 lattice_0.20-34 colorspace_1.2-7 chron_2.3-47 survival_2.39-5
[9] XML_3.98-1.4 foreign_0.8-67 DBI_0.5-1 BiocParallel_1.6.6 RColorBrewer_1.1-2 plyr_1.8.4 zlibbioc_1.18.0 munsell_0.4.3
[17] gtable_0.2.0 caTools_1.17.1 DESeq2_1.12.4 latticeExtra_0.6-28 GGally_1.2.0 geneplotter_1.50.0 AnnotationDbi_1.34.4 Rcpp_0.12.7
[25] KernSmooth_2.23-15 acepack_1.3-3.3 xtable_1.8-2 readr_1.0.0 scales_0.4.0 gdata_2.17.0 Hmisc_3.17-4 annotate_1.50.1
[33] XVector_0.12.1 gplots_3.0.1 gridExtra_2.2.1 ggplot2_2.1.0 stringi_1.1.2 dplyr_0.5.0 grid_3.3.1 tools_3.3.1
[41] bitops_1.0-6 magrittr_1.5 lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2 RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.5
[49] tidyr_0.6.0 Matrix_1.2-7.1 data.table_1.9.6 assertthat_0.1 reshape_0.8.5 R6_2.2.0 rpart_4.1-10 nnet_7.3-12

Thank you in advance!

lpantano · 2016-10-20T13:34:57Z

Hi,

sorry about this.

can you send me one of the files so I can make sure is not a problem of isomiRs version. You can try to install to last version of the package but I think 1.1.5 was the one that fixed this error.

thanks!

On Oct 20, 2016, at 3:51 AM, simonas-j notifications@github.com wrote:

isomiRs_1.1.5

simonas-j · 2016-10-21T07:27:46Z

Sorry, for disturbing you. I fixed the problem. I didn't have frequencies in miraligner's .mirna file which caused the problem.

lpantano · 2016-12-08T20:58:21Z

Let me know if you have more issues in the future

hmkim mentioned this issue Apr 28, 2016

IsomirDataSeqFromFiles error lpantano/seqcluster#14

Closed

hmkim closed this as completed May 26, 2016

hmkim reopened this May 26, 2016

lpantano closed this as completed Dec 8, 2016

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IsomirDataSeqFromFiles error #2

IsomirDataSeqFromFiles error #2

hmkim commented Apr 28, 2016

lpantano commented Apr 28, 2016

lpantano commented Apr 28, 2016

hmkim commented Apr 30, 2016 •

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hmkim commented May 25, 2016 •

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lpantano commented May 25, 2016

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simonas-j commented Oct 20, 2016

lpantano commented Oct 20, 2016

simonas-j commented Oct 21, 2016

lpantano commented Dec 8, 2016

IsomirDataSeqFromFiles error #2

IsomirDataSeqFromFiles error #2

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hmkim commented Apr 28, 2016

lpantano commented Apr 28, 2016

lpantano commented Apr 28, 2016

hmkim commented Apr 30, 2016 • edited Loading

hmkim commented May 25, 2016 • edited Loading

lpantano commented May 25, 2016

hmkim commented May 26, 2016 • edited Loading

lpantano commented May 26, 2016

hmkim commented May 30, 2016

novel miRNA by mirdeep2

total miRNA expression

lpantano commented May 30, 2016

hmkim commented May 31, 2016 • edited Loading

simonas-j commented Oct 20, 2016

lpantano commented Oct 20, 2016

simonas-j commented Oct 21, 2016

lpantano commented Dec 8, 2016

hmkim commented Apr 30, 2016 •

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