How to combine probeset expression values to gene expression value?
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5.1 years ago
cndl ▴ 50

Good morning everyone,

I have been working on Human GeneST chips (Affymetrix) for a few months now and I came into a simple problem : how do we combine the exon information into gene information ?

I am not interested in alternative transcript information, I just want to know which genes are UP/DOWN regulated between my two conditions.

Online, I found this answer « everyone has their own favorite way of combining probesets » (median, mean, standard deviation etc), which is not really helpful for a newbie like me! I also found this question : "How to combine expression values of multiple probes for one gene?" ( How to combine expression values of multiple probes for one gene? ) on the forum but I am not interested in a R package, I want to find the most accurate way to combine probesets.

So my questions are :

  • How do you usually combine probesets into genes ?

  • Before or after doing the differential expression ?

  • Do you have scientific reviews/papers treating this question (or which could help me choose a probeset selection) ?

And more widely, when analysis RNA-seq for e.g, same question, how do you do a synthesis of the exon info to the gene level? Where can I find papers about this?

I am sorry if this question seems trivial to some of you but I could not find a real consensus on this question online so I was hoping I could find some trails to follow here ! (I surely missed something !!)

Hope my questions were clear enough, do not hesitate if you need me to reformulate or elaborate!

Thank you very much for your time and answers!

RNA-Seq Gene probeset exon Affy • 1.4k views

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