Dear all,

I have been wondering which genes we are supposed to use for the PAGE analysis on AgriGO. Indeed, some papers say that they only use the DEGs of all the samples they have and some others use all the dataset since PAGE model uses a parametric statistics to get the p-values. In the end, what is the best ? I have tried both and I do not get the same results. The interpretation could be different according to the input gene list I use.

Does anyone know ?

Thanks in advance !