[BioC] Gostats with Yeast annotation
toedling at ebi.ac.uk
Tue Jul 22 15:58:33 CEST 2008
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:
> 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:
> 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
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Phone +44(0)1223 492566
Email toedling at ebi.ac.uk
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