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  • #16
    Originally posted by ygc_hku View Post
    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.

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