I have RNA-Seq data with 100 samples and 30k genes. Samples as columns and genes as rows. Tumor vs Normal.
After filtering step I see around 19k genes were used for differential analysis. With differential analysis cutoff FC > 2 and FDR < 0.05, there are about 1000 differential expressed genes.
I'm going to use foldchange and Pvalue for ranking the genes and input for GSEA
For Gene set enrichment analysis do I need to use only those 1000 differential expressed genes or do I need to use those 19k genes as input?