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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
