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]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Best wishes > Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor