[BioC] DEXSeq error

[Wolfgang Huber]

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