[BioC] Gostats with Yeast annotation

[Robert Gentleman]

Hi Alex,
   If you are willing to use R-devel and Bioc-devel, the issue should be 
fixed there.  I would be interested in hearing of any problems you might 
have (or successes) using that version.  I am waiting for some reports 
of success before I port this to release,

best wishes
   Robert


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 

the man page is pretty explicit, (?org.Sc.sgdGO)

      Mappings were based on data provided by: Yeast Genome (
      ftp://genome-ftp.stanford.edu/pub/yeast/data_download ) on
      2008-Mar29

  I am not sure what more we could put there.

best wishes
   Robert

> 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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org