[BioC] DEXSeq analysis for paired samples

[Simon Anders]

Hi Philip

On 10/01/14 15:45, Philip Jonsson wrote:
[...]

> formula1 = ~ sample + exon + experiment:exon + condition:exon
> formula0 = ~ sample + exon + experiment:exon
> 
> ecs = estimateDispersions(ecs, minCount=5, nCores=cn, formula=formula1)
> ecs = testForDEU(ecs, nCores=cn, formula0=formula0, formula1=formula1)
> 
> Is this the correct way to account for the paired nature of my samples?

Yes, this is correct.

One point: Make sure that 'experiment' is interpreted as a factor and
not as an integer vector.

  Simon