Hi, I run the example of read.HTSeqCounts() from DEXSeq, get following Error: Error: all(unlist(lapply(design, class)) == "factor") is not TRUE Any suggestion? Thanks in advance. Regards, Sheng code: library(DEXSeq) inDir = system.file("extdata", package="pasilla", mustWork=TRUE) annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") samples = data.frame( condition = c(rep("treated", 3), rep("untreated", 4)), replicate = c(1:3, 1:4), row.names = dir(system.file("extdata", package="pasilla", mustWork=TRUE), pattern="fb.txt"), stringsAsFactors = TRUE, check.names = FALSE ) annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)), design = samples, flattenedfile = annotationfile) sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DEXSeq_1.3.16 Biobase_2.17.6 BiocGenerics_0.3.1 loaded via a namespace (and not attached): [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.13.2 hwriter_1.3 plyr_1.7.1 statmod_1.4.15 stringr_0.6.1 [[alternative HTML version deleted]]

Dear Sheng, From a recent version of DEXSeq, the design data frame needs to have ONLY factors on it. I owe you an apology since I forgot to update the example. I just updated it right now: library(DEXSeq) inDir = system.file("extdata", package="pasilla", mustWork=TRUE) annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") samples = data.frame( condition = c(rep("treated", 3), rep("untreated", 4)), row.names = dir(system.file("extdata", package="pasilla", mustWork=TRUE), pattern="fb.txt"), stringsAsFactors = TRUE, check.names = FALSE ) annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)), design = samples, flattenedfile = annotationfile) Best wishes, Alejandro > Hi, > > I run the example of read.HTSeqCounts() from DEXSeq, get following Error: > > Error: all(unlist(lapply(design, class)) == "factor") is not TRUE > > Any suggestion? Thanks in advance. > > Regards, > Sheng > > > code: > > library(DEXSeq) > inDir = system.file("extdata", package="pasilla", mustWork=TRUE) > annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") > samples = data.frame( > condition = c(rep("treated", 3), rep("untreated", 4)), > replicate = c(1:3, 1:4), > row.names = dir(system.file("extdata", package="pasilla", mustWork=TRUE), > pattern="fb.txt"), > stringsAsFactors = TRUE, > check.names = FALSE > ) > > annotationfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff") > > > ecs = read.HTSeqCounts(countfiles = file.path(inDir, rownames(samples)), > design = samples, > flattenedfile = annotationfile) > > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DEXSeq_1.3.16 Biobase_2.17.6 BiocGenerics_0.3.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.91-1 XML_3.9-4 biomaRt_2.13.2 hwriter_1.3 plyr_1.7.1 > statmod_1.4.15 stringr_0.6.1 > > [[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