4.6 years ago by
University of Bergen, Norway
If I understand it correctly, you simply want to find the unique gene identifiers (or probe ids) that are differentially expressed in all experiments? One simple way to do that in R would be (here for three sets):
a = c('gene1','gene3','gene5','gene7','gene9')
b = c('gene3','gene6','gene8','gene9','gene10')
c = c('gene2','gene3','gene4','gene5','gene7','gene9')
 "gene3" "gene9"
On a side note, if you are requiring a gene to be significantly differentially expressed in all experiments, that is a fairly tough threshold. Since experiments typically do not have the power to detect all genes that are truly differentially expressed, you are likely to miss some in each set due to randomness. You could, alternatively, require that a gene is significantly differentially expressed in some samples, and has a fold change in the same direction (or over some meaningful threshold) in others.