[BioC] Understanding GOstats
James W. MacDonald
jmacdon at med.umich.edu
Wed Mar 19 14:34:40 CET 2008
alex lam (RI) wrote:
> Dear colleagues,
> I would like to check if my understanding onone aspect of GOstats is
> 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?
Yes. Although this particular probeset isn't mapped directly to the
parent GO term, it _is_ by definition mapped to that term since the
child term is a subset of the parent (here subset being defined by
either an is_a or a part_of relationship to the parent).
Note that this will be true even if conditional = TRUE, unless
GO:0002474 is significant _and_ that particular probeset contributed to
that significance. Although we shouldn't be talking about probesets here
because the GO analysis is done on the gene level.
> 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?
Good question, but wrong forum. We just repackage existing annotations,
and as far as I can tell everybody says the same thing about this gene.
For instance, NCBI:
The same thing is true of Affy and Ensembl.
> Many thanks,
> Alex C. Lam
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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