[BioC] DEXSeq troubles

[Alejandro Reyes]

Dear Margaret,

The error is because you are only using one file, and I agree that the 
error message should be more informative.

What do you intend to do with DEXSeq using only one sample? DEXSeq is 
designed to identify differences in exon usage of at least two 
conditions with samples with replicates (which means that you need a 
minimum of 4 files with counts).

Best regards,
Alejandro

> 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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>
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