[BioC] DEXSeq error during fold change calculation
Beth [guest]
guest at bioconductor.org
Mon Apr 9 19:05:52 CEST 2012
I am interested in detecting splicing differences between 2 conditions, with 5 biological replicates of each, and DEXSeq seems like a good tool for the job.
> ABsamples
condition replicate
A013 A 1
A014 A 2
A015 A 3
A016 A 4
A017 A 5
B013 B 1
B014 B 2
B015 B 3
B016 B 4
B017 B 5
I generated an exon count matrix for non-overlapping Ensemblv64 exon parts using the provided dexseq_prepare_annotation.py and BEDtools. (I used Tophat for alignment.)
As far as I can tell, the ExonCountSet was created successfully from this input
> ABMatrix <- read.table(file="ABExonsMatrix.txt")
> ABgeneExonIDs <- read.table(file="ABExonIDs.txt")
> ABsamples <- read.table("ABsamples.txt")
> ABExon <- newExonCountSet(countData = ABMatrix, design = ABsamples, geneIDs = ABgeneExonIDs$V2, exonIDs = ABgeneExonIDs$V1)
I proceeded to this step:
> AB013to017 <- makeCompleteDEUAnalysis(ABExon, nCores=22)
and the "Estimating Cox-Reid exon dispersion estimates" and the "Testing for differential exon usage" steps also looked like they worked (though there were a few errors like this for some of the exons "Error in chol.default(XVX + lambda * I) : the leading minor of order 10 is not positive definite", but I am pretty sure that isn't my underlying problem)
But then this happened:
Calculating fold changes using 22 cores. (Progress report: one dot per 100 genes)
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "fData", for signature "try-error"
In addition: Warning message:
In mcLapply(allecs, FUN = funtoapply, mc.cores = mc.cores) :
all scheduled cores encountered errors in user code
I am not a very experienced R user, so I am not sure if this error stems from problems with my dataset, problems with the underlying R environment, or a problem with DEXSeq itself.
I would appreciate any thoughts and feedback you may have. Please let me know if I should provide additional information and I would be happy to do so.
Thanks for your time,
Beth
-- output of sessionInfo():
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] multicore_0.1-7 DEXSeq_1.0.2 Biobase_2.14.0
[4] BiocInstaller_1.2.1
loaded via a namespace (and not attached):
[1] hwriter_1.3 plyr_1.7.1 statmod_1.4.14 stringr_0.6 tools_2.14.2
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