[rozitaa]

You may interesting in using clusterProfiler package: http://www.bioconductor.org/packages...rProfiler.html

Hi,

I am using clusterProfiler but seems some of the functions like gseGO(), getGeneSet() or enrichMap() have been removed from this package since it couldn't be found.

Another issue is, I have two gene lists with 280 and 909 genes in them. but I am only able to get one GO(BP) significant category for both!!! Whereas when I work with david I get so much different ones. Is there any thing wrong in my code:
enrichGO(gene=gene_Lpos_test_colon_exp1_entrezID, organism="mouse", ont="BP", pvalueCutoff=0.05, pAdjustMethod='fdr', qvalueCutoff=0.1, universe=background_genes , minGSSize=3, readable=T)

Thanks.