[BioC] DEXSeq - identical p-values for all exons in a gene

[Simon Anders]

Hi

In your code

>> ecs <- read.HTSeqCounts(countfiles=countFiles, design=sampleTable, flattenedfile=annotationfile)
>> ecs <- estimateSizeFactors(ecs)
>> ecs <- estimateDispersions(ecs, formula=formulaFullModel, nCores=cores, quiet=FALSE, file='dexseq_progress_report.txt')
>> ecs<- fitDispersionFunction(ecs)
>>
>> ecs <- testForDEU(ecs, formula0=formulaReducedModel, formula1=formulaFullModel, nCores=cores, quiet=FALSE, file='testforDEU_progress_report.txt')

you specify the full model formula in 'testForDEU' but do not in
'estimateDispersions'.

You have noticed that we changed the way how formulae should be
specified. Before, you needed three formulae, now only two, because we
got rid of the need for a special "dispersion formula". Rather, you use
the full model formula for dispersion estimation, too.

However, you have to pass the formula to _both_ functions.

  Simon