[BioC] Yeast annotations

Marc Carlson mcarlson at fhcrc.org
Mon Mar 3 18:18:24 CET 2008

Devarajan, Karthik wrote:
> Hello,
> I'm trying to apply enrichment analyses to gene lists obtained from
> yeast data using GOstats. I want to use the Yeast GO slim annotation to
> do the analysis. My yeast data is from the SGD database and it is not
> clear to me which annotation package I should use. The package
> org.Sc.sgd.db is not supported yet and the YEAST package does not seem
> to contain the required probe names. Does anyone have any idea what
> FIXME (mentioned in the Bioconductor help file for YEAST) refers to? I'd
> appreciate any input regarding this issue.
> Thanks,
> K
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Hi Karthik,

I would like to try and help you but I need a lot more information. 
What is your sessionInfo()?  And what specifically is not supported that
you want to do?  In general I recommend for people to use the newer
org.Sc.sgd.db packages for organism based annotations.  These packages
should emulate all the same functionality as the older annotations
packages that they are replacing (in this case YEAST is being replaced
by org.Sc.sgd.db). 


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