[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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