Hi- I have a new DEXSeq error that I could use help with: > samples=data.frame( + condition=c(rep("myfile", 1)), + row.names=file.path("/home/mlinan", pattern="myfile.counts"), + stringAsFactors=FALSE, + check.names= FALSE) > ecs = read.HTSeqCounts(countfiles = rownames(samples), design=samples, + flattenedfile=file.path("/home/mlinan", "myfile.gff") + ) Error in strsplit(rownames(dcounts), ":") : non-character argument > > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] DEXSeq_1.6.0 Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] Biostrings_2.28.0 GenomicRanges_1.12.4 IRanges_1.18.1 [4] RCurl_1.95-0.1.2 Rsamtools_1.12.3 XML_3.96-1.1 [7] biomaRt_2.16.0 bitops_1.0-5 hwriter_1.3 [10] statmod_1.4.17 stats4_3.0.1 stringr_0.6.2 [13] zlibbioc_1.6.0 My count file does have " : " symbol, here is a brief example: ENSMMUG00000098993:001 0 ENSMMUG00000098994:001 0 _ambiguous 3145 _empty 2488107 _lowaqual 479881 _notaligned 0 Thanks, Margaret Linan [[alternative HTML version deleted]]

Dear Margaret, The error is because you are only using one file, and I agree that the error message should be more informative. What do you intend to do with DEXSeq using only one sample? DEXSeq is designed to identify differences in exon usage of at least two conditions with samples with replicates (which means that you need a minimum of 4 files with counts). Best regards, Alejandro > Hi- > > I have a new DEXSeq error that I could use help with: > >> samples=data.frame( > + condition=c(rep("myfile", 1)), > + row.names=file.path("/home/mlinan", pattern="myfile.counts"), > + stringAsFactors=FALSE, > + check.names= FALSE) >> ecs = read.HTSeqCounts(countfiles = rownames(samples), design=samples, > + flattenedfile=file.path("/home/mlinan", "myfile.gff") > + ) > Error in strsplit(rownames(dcounts), ":") : non-character argument >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] DEXSeq_1.6.0 Biobase_2.20.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] Biostrings_2.28.0 GenomicRanges_1.12.4 IRanges_1.18.1 > [4] RCurl_1.95-0.1.2 Rsamtools_1.12.3 XML_3.96-1.1 > [7] biomaRt_2.16.0 bitops_1.0-5 hwriter_1.3 > [10] statmod_1.4.17 stats4_3.0.1 stringr_0.6.2 > [13] zlibbioc_1.6.0 > > My count file does have " : " symbol, here is a brief example: > ENSMMUG00000098993:001 0 > ENSMMUG00000098994:001 0 > _ambiguous 3145 > _empty 2488107 > _lowaqual 479881 > _notaligned 0 > > Thanks, > Margaret Linan > > [[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