Hi, I have what I think are three simple questions regarding the goana() function of edgeR, which I am not very familiar with:
1-Does it work with Arabidopsis?
2- I understand that if the coefficient you are looking into is cond.B - cond.A, you'd be fishing out terms that are differently represented between B and A, if I am right. What if you want to compare GO terms from DE genes in cond.B - cond.A against the GO terms from the whole genome or from all genes in the dataset?
3-If looking into cond.B - cond.A will render terms that are differently represented between B and A, what if you are looking into an interaction-type contrast such as (cond.A1 - cond.B1) - (cond.A0 - cond.B0). What would be the interpretation of goana results?
Thanks a lot for any help you may provide me with on those.