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Showing more terms in the result of GESA by ClusterProfiler

Hi

I've been working on the gene set enrichment analysis by ClusterProfiler, and I'm able to generate the enriched terms table by the enricher function:

CRE_MapMan_GSEA <-enricher(DEG_cht7_6_up_LocusID$Gene_ID,
                           TERM2GENE=TERM2GENE, 
                           TERM2NAME = TERM2NAME,
                           pvalueCutoff = 0.05)

Result:

  ID               Description                              pvalue

    28.1           DNA.synthesis/chromatin structure        6.96E-19
    31.6.1.1       cell.motility.eukaryotes.basal bodies    4.77E-08
    28.2           cell.motility.eukaryotes.basal bodies    1.63E-06
    24             DNA.repair                               4.38E-06
    31.2           Biodegradation of Xenobiotics            1.32E-05
    27.3.44        cell.division                            1.90E-03
    31.1           RNA.regulation of transcription.         2.24E-03
                   Chromatin Remodeling Factors

However, there're only 7 terms displayed. Does that mean the rest of them are not significant enough? Is there any way I can see the p-values of more terms? I've tried to play with the pvalueCutoff parameter, but the number of the displayed term is still the same.

Thanks!

clusterprofiler r bioconductor

1 answer

Try to use different qvalueCutoff value as cut off.

It worked! Thank you very much!

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