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.

Thanks

When you run rma() on your data, what you end up getting ARE the expression values (which is what I believe you mean by 'expression indices'). In other words, the values are the summarized, estimated levels of expression for each transcript that the HTA array measures. To get DE genes you then compare your groups using something like the limma package.