Hello, I have a function data sets. I want to look at which functions are over-representative. However, I am only interested in a subset of functions for example DNA synthesis.

Can I just use the functions related to DNA synthesis (subset table) to do the DESeq2 analysis or I have to use the whole dataset and later found which over-representative functions relative to DNA synthesis?

Thanks,

Hi,

For DESeq2, it's not advised to only run on a subset of genes which might be "interesting". This is because the software needs to look across "un-interesting" genes as well to estimate parameters (size factors, for example).