[BioC] DEXSeq error during fold change calculation

[Wolfgang Huber]

Dear Beth

thank you for the feedback and detailed problem description! Can you try 
again with a more recent version of DEXSeq e.g. 
http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html
(better even, the 'devel' version since the package is still continously 
being improved.)

You have been using a relatively old and dusty version of DEXSeq, and I 
believe that there was a bug in the code that caused messages like the 
one you report (not leading to false results, but to fatal errors during 
the execution), and which has since long been fixed.

Please let us know how it goes with the newer version.

	Best wishes
	Wolfgang

Apr/9/12 7:05 PM, Beth [guest] scripsit::
>
> 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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>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber