[BioC] DEXSeq error

[Alejandro Reyes]

Dear Chuming Chen,

Thanks for the report, it was not so clear to me in which part of your 
code the error message comes out, but I think it is in DEXSeqHTML is 
that correct?

I tried to reproduce an error with the line that appears there but I 
could not. Could you try updating to a newer version of DEXSeq? Or could 
you send me your ecs (or a subset of it containing the gene that 
generates that error)?

Alejandro Reyes



> Hi All,
>
> I am trying to use DEXSeq to find out differential exon usage and encounter the following error. I have included the session info and my R script.
>
> Could you please help me finding out what could be the problem?
>
>
> Estimating Cox-Reid exon dispersion estimates using 30 cores. (Progress report: one dot per 100 genes)
> ........................................................................................................................Testing for differential exon usage using 30 cores. (Progress report: one dot per 100 genes)
> ........................................................................................................................Error in pmax(which(decade_lengths > 0.1), 0) :
>    cannot mix 0-length vectors with others
>
> The session info is below.
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] DEXSeq_1.2.0       Biobase_2.16.0     BiocGenerics_0.2.0 multicore_0.1-7
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1   XML_3.9-4      biomaRt_2.12.0 hwriter_1.3    plyr_1.7.1
> [6] statmod_1.4.14 stringr_0.6
>>
>
> My R script is below:
> $ more run-FL-LL-12-fdr-0.05.R
> library(multicore)
> library(DEXSeq)
> annotationfile = file.path("Gallus_gallus.WASHUC2.64.clc.gff")
> samples = data.frame(
> 	condition = c(rep("FL", 12), rep("LL", 12)),
> 	replicate = c(1:12, 1:12),
> 	row.names = dir("clcExonCountFiles", full.names=TRUE, pattern=".count"),
> 	stringsAsFactors = TRUE,
> 	check.names = FALSE
> )
> ecs = read.HTSeqCounts(countfiles = file.path(rownames(samples)), design = samples, flattenedfile = annotationfile)
> ecs = estimateSizeFactors(ecs)
> ecs = estimateDispersions(ecs, nCores=30)
> ecs = fitDispersionFunction(ecs)
> ecs = testForDEU(ecs, nCores=30)
> DEXSeqHTML(ecs, geneIDs=NULL, path="report/FL-LL-12/FDR-0.05", file = "FL-LL-DEU-fdr0.05.html", fitExpToVar="condition", FDR=0.05, color=NULL, color.samples=NULL)
> 	[[alternative HTML version deleted]]
>
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