[BioC] ChrMapHyperGParams and linearMTest in Category

Daren Tan darentan76 at gmail.com
Sat Apr 4 05:28:32 CEST 2009

Beyond the scope of the manual and vigenettes of Category and GOStats,
I would like to understand more about ChrMapHyperGParams and

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 ?

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