Hello everyone! I have a question about which Background to use for the Gene Ontology Analysis of the DEGs obtained by RNA-Seq. According to the instructions on the GO website:
" The reference list should be the list of all the genes from which your smaller analysis list was selected. For example, in a list of differentially expressed genes, the reference list should only contain genes that were detected at all in the experiment, and thus potentially could have been on a list of genes derived from the experiment."
In this context, I'm using the list of genes obtained by the exactTest() function of edgeR, which gives a list based on "pseudo - counts". Since this "pseudo-counts" are for internal use of edgeR pipeline, I don´t know if it is adequate in this case. Any thoughts?