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!