[BioC] Understanding GOstats

[alex lam (RI)]

Dear colleagues,

I would like to check if my understanding onone aspect of GOstats is
correct.

The probeset 1370428_x_at is linked to the GO term GO:0002474

When I use hyperGTest (with conditional=F), if this probeset is DE,
enrichment of GO:0002474 will be tested. And so will its parent GO term
GO:0048002, even this GO term is not explicitly linked to the affy id in
the annotation. Is that correct? GOstats will follow the GO tree from
bottom-up to conduct tests?

On a slightly different matter, the grandparent node of GO:0002474,
GO:0019882, is explicitly linked to this affy id in the annotation. Why
is this so, but not the parent node GO:0048002?

Many thanks,
Alex

--------------------------------------------
Alex C. Lam
Roslin Institute (Edinburgh)
Midlothian
EH25 9PS
United Kingdom
Tel: +44 131 5274471

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