Entering edit mode
7 months ago
yxwucq
•
0
I need to test whether a particular gene set is upregulated in my data. First, I have to provide a sorted ranked background gene set like this:
gene_name logfc
xx 3.0
yy 2.0
I can get this ranked list from different expression analysis, but do I need to filter out insignificant genes (based on p-value or logfc) in advance? Or just provide all detected genes?
no filtering for GSEA other than filtering of low expressed genes for your differential expression analysis.
The following paper offers some additional insights: Urgent need for consistent standards in functional enrichment analysis