[BioC] DEXSeq error during fold change calculation

[Beth [guest]]

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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