[BioC] Gostats with Yeast annotation

Alex Gutteridge alexg at ruggedtextile.com
Tue Jul 22 15:37:14 CEST 2008


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

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