[BioC] topGO sensitive to the order of "interesting" gene ids
Wolfgang Huber
whuber at embl.de
Fri Jan 21 01:49:52 CET 2011
Hi Paul
the author of the package might have more substantive things to say, but
can you provide a self-contained piece of example code that demonstrates
your observation, as well as the output of 'sessionInfo()'? This will
probably be essential to enable anyone to pick up your observation and
explain and/or debug it.
Wolfgang
Il Jan/19/11 6:27 PM, Paul Rigor ha scritto:
> Hi all,
>
> I wasn't sure whether I should have posted this on the list, but I think
> we've discovered some odd behavior with topGO.
>
> Given a set of the same (but differently ordered) list of uniprot id's, we
> are getting different enrichment results. I wasn't sure whether the ordering
> mattered. Or does the ordering hinge upon the ranking of the p-values? We
> are just looking for GO enrichment in non-microarray studies, btw, so we've
> faked the p-values (eg, 0.001) for the set of interesting genes.
>
> Thanks,
> Paul
>
> [[alternative HTML version deleted]]
>
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--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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