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

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