[BioC] ChrMapHyperGParams and linearMTest in Category

Daren Tan darentan76 at gmail.com
Tue Apr 7 11:29:44 CEST 2009

Hope someone or the developer of GOStats/Category can answer my queries.

On Sat, Apr 4, 2009 at 11:28 AM, Daren Tan <darentan76 at gmail.com> wrote:
> Beyond the scope of the manual and vigenettes of Category and GOStats,
> I would like to understand more about ChrMapHyperGParams and
> linearMTest.
> After successfully using "GOHyperGParams" and "KEGGHyperGParams" with
> platform-independent annotation database "org.Hs.eg.db", I tried to do
> the same with "ChrMapHyperGParams" but kept getting error messages
> that "org.Hs.egENTREZID" couldn't be found. This was unexpected as I
> couldn't fanthom why ChrMapHyperGParams would need probes information.
> I would like to get around this problem even with "org.Hs.eg.db" so
> that my enrichment analysis would be complete for GO/Pathway/CHR.
> hyperGTest and linearMTest use hypergeometric distribution and linear
> model respectively as their names implied. What situations will either
> tests be more suitable for ? Would both tests at same p-value cutoffs
> give similar results ? Should I even favour hyperGTest or linearMTest
> ?
> Previously, I used david and panther and wondered is it appropriate to
> get FDR based on bonferroni-tests from the p-values of hyperGTest and
> linearMTest. Would FDR be meaningful for GO/Pathway/CHR enrichment
> analysis ?

More information about the Bioconductor mailing list