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

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