[BioC] DEXSeq error

[Chuming Chen]

Hi Alejandro,

Thanks a lot for your quick reply! Please see my answers to your questions below.

On Jul 6, 2012, at 12:33 PM, Alejandro Reyes wrote:

> 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?

Yes. It is in DEXSeqHTML step. Actually, the image files and related html files have been created in the "files" folder. But the summary table on the FL-LL-DEU-fdr0.05.html were not created.

> 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?

I am using DEXSeq_1.2.0. Is this the latest version? Where can I get the newer version?


> Or could you send me your ecs (or a subset of it containing the gene that generates that error)?
> 

You can find my ecs at http://www.eecis.udel.edu/~chenc/DEXSeq/ecs.Rdata


Thanks again.

Chuming

> 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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> 
>