[BioC] Gostats with Yeast annotation

[Marc Carlson]

Hi Alex,

You can see the sources used to make the org.Sc.eg.db package by calling 
its dbInfo() function like this:

org.Sc.sgd_dbInfo()

You can see that there are 3 sources of information listed for this 
package. To make the GO to yeast mappings, the mappings themselves come 
from SGD as listed in the help pages.

Hope this helps,

Marc




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
>
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