[BioC] DEXSeq error

[Chuming Chen]

Dear Wolfgang,

I have downloaded DEXSeq 1.3.9 and tested using my data. Everything is fine now.

Thanks for this nice tools and quick fix.

Chuming

On Jul 12, 2012, at 7:57 AM, Wolfgang Huber wrote:

> Dear Chuming
> 
> Thank you for your message. The current version of DEXSeq is 1.3.9:
> http://www.bioconductor.org/packages/devel/bioc/html/DEXSeq.html
> 
> Can you try again with that, and report to us if the error persists?
> 
> 	Best wishes
> 	Wolfgang	
> 
> On 7/6/12 9:33 PM, Chuming Chen wrote:
>> 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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>>>> 
>>> 
>>> 
>> 
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> 
> 
> -- 
> Best wishes
> 	Wolfgang
> 
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
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