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Statistics of count data for differential expression
2 messages · Vishal Thapar, Ben Bolker
Vishal Thapar <vishalthapar <at> gmail.com> writes:
This is more of a general statistics question that I am not so sure about so I need some thoughts from you experts out there. I have Chip-Seq read count data for 2 different treatments (T1 and T2) and my final aim is to calculate differential expression between them. I also have Chip-Seq read count data from a "control / wild type (C)" experiment. I have 3 replicates (2 technical, 1 biological) of each of these. What is the best way to go for a differential expression between T1 and T2? Is it best to just go straight between T1 and T2 or is it to do a T1vsC and T2vsC and then compare the results from these for diff expr? What do you think is better and why? I appreciate your thoughts on this.
Offhand I don't see why you need to involve the wild type if you are really interested in differential expression between T1 and T2, but I think you might get a more informed answer on the Bioconductor list ... Ben Bolker