Question: DEXSeq error during fold change calculation
7.5 years ago by
Guest User • 12k
Guest User • 12k wrote:
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:  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  LC_PAPER=C LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  multicore_0.1-7 DEXSeq_1.0.2 Biobase_2.14.0  BiocInstaller_1.2.1 loaded via a namespace (and not attached):  hwriter_1.3 plyr_1.7.1 statmod_1.4.14 stringr_0.6 tools_2.14.2 -- Sent via the guest posting facility at bioconductor.org.
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