Hi Everyone, I encountered an error message from DEXSeq, and would like to know if someone else encountered it too and how they were able to fix the problem. Below is my code and error message: I have come across the following error. How do I prevent the error from occuring? Is it ok to use stringsAsFactors=FALSE ? What is meant by factors? > setwd("C:/Users/mlinan/Counts") > samples=data.frame(condition=c(rep("Two", 2), rep("Four", 2)), + row.names=dir(path="C:/Users/mlinan/Counts", pattern="ah.counts"), + stringAsFactors=TRUE, check.names=FALSE) > ecs=read.HTSeqCounts(countfiles=rownames(samples), design=samples, + flattenedfile=file.path("C:/Users/mlinan/Desktop/Counts", "My_file.gff")) *Error: all(unlist(lapply(design, class)) == "factor") is not TRUE* * * > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods 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] biomaRt_2.16.0 Biostrings_2.28.0 bitops_1.0-5 GenomicRanges_1.12.4 hwriter_1.3 [6] IRanges_1.18.1 RCurl_1.95-4.1 Rsamtools_1.12.3 statmod_1.4.17 stats4_3.0.1 [11] stringr_0.6.2 XML_3.96-1.1 zlibbioc_1.6.0 > Thanks, Margaret Linan [[alternative HTML version deleted]]