Hi, I have used DEXSeq (version 1.2.0) successfully to find differentially expressed exons in RNA-seq data. Yesterday I upgraded DEXSeq to version 1.3.13 I get the following error: > ecs=read.HTSeqCounts(countfiles=file.path("/data/DexSeqCounts/",past e(rownames(samples),"txt",sep=".")),design=samples,flattenedfile=annot ationfile) Error: all(unlist(lapply(design, class)) == "factor") is not TRUE Thank you in advance. Regards, Nirmala [[alternative HTML version deleted]]

Dear Nirmala, Yes, it is a recent change in DEXSeq, just make sure that all the columns of your "samples" are factors. Alejandro > Hi, > > I have used DEXSeq (version 1.2.0) successfully to find differentially expressed exons in RNA-seq data. Yesterday I upgraded DEXSeq to version 1.3.13 I get the following error: > >> ecs=read.HTSeqCounts(countfiles=file.path("/data/DexSeqCounts/",pas te(rownames(samples),"txt",sep=".")),design=samples,flattenedfile=anno tationfile) > Error: all(unlist(lapply(design, class)) == "factor") is not TRUE > > Thank you in advance. > > Regards, > Nirmala > > > > [[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 >