Dear Margaret, Could you please add the first lines of your res1 object (e.g. head)? Best regards, Alejandro > Dear Alejandro, > > I have been having success with the pasilla exercise, but have noticed > that plotMA > does not output the same graph as what is depicted in the vignette. > > I've tried the plotMA code after loading DEXSeq and DESeq but the > graph appears the same, > the warning message is the same too. > > plotMA code with warning: > > > plotMA(with(res1, data.frame(baseMean = meanBase, > > + log2FoldChange = > ?log2fold(untreated/treated)?, > > + padj = padjust)), > > + ylim=c(-4,4), cex= 0.8) > > Warning messages: > > 1: In Ops.factor(mmm, each) : > not meaningful for factors > > 2: In Ops.factor(py, ylim[1]) : < not meaningful for factors > > > > Inline image 1 > Thanks, > ML > > > On Sun, Jun 2, 2013 at 3:06 AM, Alejandro Reyes > <alejandro.reyes at="" embl.de="" <mailto:alejandro.reyes="" at="" embl.de="">> wrote: > > 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 <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >