[BioC] Gostats with Yeast annotation

Joern Toedling toedling at ebi.ac.uk
Tue Jul 22 15:58:33 CEST 2008

Hi Alex,
afraid I cannot your questions about the yeast annotation package, but I 
would like to mention that alternatively you could create a simple list 
mapping gene identifiers to GO identifiers using the biomaRt package to 
query the up-to-date annotation in the Ensembl data base and use this 
list to do the same analysis using the topGO package. The topGO package 
has a slightly different interface to set up the test, but the vignette 
provides a good working example.
Hope this helps.

Alex Gutteridge wrote:
> Hi,
> I've been trying to use the hyperGTest method from the GOstats package 
> with some yeast ORF data. I notice in this thread from a month or so 
> ago that there are problems at the moment with using any of the yeast 
> annotation sets apart from 'YEAST' (which is deprecated) due to 
> missing ID2EntrezID methods:
> https://stat.ethz.ch/pipermail/bioconductor/2008-June/022697.html
> I just wanted to make sure that this was still the case and I guess 
> fish around for an estimated ETA for when the org.Sc.sgd.db 
> annotations (which are replacing YEAST as I understand it) will be 
> compatible with hyperGTest?
> Also, is the exact source of GO annotations used in these packages 
> documented anywhere? Looking in the DESCRIPTION file I see 'primarily 
> based on mapping using ORF identifiers from SGD' for org.Sc.sgd.db and 
> 'assembled using data from public data repositories' for YEAST. Should 
> I just take it these are based on the SGD GO annotation file from the 
> date given in the Packaged field of the DESCRIPTION file? For YEAST 
> there is also a Created field which is aprox. 1 month prior to the 
> Packaged date so I'm guessing the real age of the data is that one? 
> The yeast annotations change so quickly it's useful to be able to pin 
> this down as accurately as possible.
> Thanks in advance for any help with these questions.
> Alex Gutteridge
> Department of Biochemistry
> University of Cambridge

Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk

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