I have a genome of 22129 genes and I got a list of 2905 DE genes I used Goseq to perform GO enrichment analysis but got a list of more than 500 significantly enriched GO terms (p<0.05). How can I get a manageable number of enriched GO terms? Is it because the number of DE genes is too large?
Here's how I perform the enrichment analysis (bias.data - data corrected by gene length)
pwf <- nullp(gene.data, bias.data = genes.bias.data, plot.fit = FALSE) GO.wall <- goseq(pwf, gene2cat = gene2go_data, method = "Wallenius", use_genes_without_cat = FALSE)