[BioC] DEXseq: Making exonCountSet object

[Simon Anders]

Hi Elena

On 2012-02-11 02:06, Elena Sorokin wrote:
> With my own data, though, the differential expression testing doesn't
> work, and additionally, the annotation GFF file doesn't seem to have
> loaded. Could somebody kindly write out the exact code for reading in
> the HTSeq counts files using the pasilla input files (p.11 of the
> vignette), or better yet, point out where my code below is wrong?

Probably something went wrong here:

> # make exon count set object
> ecs = read.HTSeqCounts(countfiles = file.path("C:\\Rdata\\DEXseq",
> paste(paste(rownames(samples),"counts", sep="_"), "txt", sep=".")),
>                          design = samples,
>                          flattenedfile = annotationfile)

First, look at the return value of the call to file.path:

file.path("C:\\Rdata\\DEXseq", paste(paste(rownames(samples),"counts", 
sep="_"), "txt", sep="."))

If you type this without the rest around it, do you get a list of your 
file names? Are they really correct?

Also check with 'head(count(ecs))' whether the count data really made it 
into the object. Similarly, check with 'pData(ecs)' and 
'head(fData(ecd))' whether the annotation is there. And, after calling 
'estimatSizeFactors', look at the result with 'sizeFactors(ecs)'.

This should help pinpoint where things go wrong.

   Simon