I know in edgeR, in multivariate analysis, you can do "ceof=3:5" to test and get p-values for genes that are differentially expressed under ANY of the conditions specified by "coef=3:5". My understanding is that "ANY" here means OR? Meaning if a gene is differentially expressed in either condition 3 or 4 or 5 being compared to the control (constant term), then it would be shown significant as indicated by its p-value. How if I want to find DEGs that are expressed in 3 AND 4 AND 5? How to setup the parameters? I know you can make condition 3 & 4 & 5 to be one condition and test for it, but this is a little bit cumbersome. If you can use something like "coef=3:5" on the fly, it would awesome.
Thanks in advance!
By any chance, are you talking about interaction terms?
Not interaction terms. For instance, you treat a cell line with a compound of concentration 100nM, 200nM, 500nM. You want to find out if a gene 1) responds to any of the compound treatment; 2) responds to all of the compound treatment.
Does this make sense to you?
so it seems like you are expecting to make contrast specific design. In that case if you have already properly created your design matrix then it is not a problem to do the contrast specific DE test with edgeR and also do the entire estimation as well. Take a look at the links below.
link1
If you start looking at the edgeR manual from page 29, you will see that the
exactTest()
can make the classical pairwise test between your groups of interest If you intend to use the glm based approach then the successive tests are pretty well defined in the manual of edgeR from page 30 and how to set the contrast between particular groups as in case 3 vs 4,, 4 vs 5 , etc The key is to prepare themodel.matrix()
properly with the proper design of groups/levels and use contrast specific levels with glm-based approach. It should not be a problem to tackle it.I can only say this much unless I see the design of your model matrix , it is difficult to address about the specific contrasts that you intend to set.
This link is pretty informative as well but I will still advice for manual