Dear BioC community,
I am a newbie in HTA analysis and I am struggling to get the DE genes, based on the whole transcript expression.
I read and normalised the CEL files using the ram function of oligo package by setting the option target=core. So I have around 70000 probesets, but then, how can I calculate the expression indices at transcript level? Is there any function? As far as I know, featureFilter returns the probeset with the greatest variance, for a given transcript, but I need the info along the all expressed exons.