We found DE genes and then performed GO / pathway enrichment analysis (fisher exact test is used, right?)
What we are doing now is based on these two ratio: 1: number of genes in specific GO / total number of genes 2: number of DE genes in GO / total number of DE genes
Someone suggest that we should exclude genes that not express in both groups.
1: total number of genes -> total number of genes - genes that not express in both groups 2: total number of DE genes -> total number of DE genes - genes that not express in both groups
This suggestion is also kind of make sense considering genes in DE list has to be expressed in at least one group.
Can anyone share some comments? Thanks