[BioC] how often are annotation packages updated (with respect to hgu133a.db and hgu133plus2.db)

Kasper Daniel Hansen khansen at stat.berkeley.edu
Thu May 7 01:13:03 CEST 2009

As has been discussed multiple times on the list, essentially an  
annotation package is update bi-annually, in context with each  
Bioconductor release.

Let us say the release dat is April 1st. Sometime before April 1st  
(probably within a few months of this date), someone (right now I  
believe it is Marc Carlson) will generate the annotation packages for  
the most recent version of the annotation available at that date.

So first of all you need to make sure you are using the newest version  
of R. If that is not good enough, you will need to build it from  
scratch yourself.

I would be surprised if you find many discrepancies, given that  
Bioconductor was released very recently. But I am also not up to date  
on Affy's release cycle for their annotation.


On May 6, 2009, at 15:00 , Andrew Yee wrote:

> Hi, a naive question that relates to the annotation data packages:   
> how
> often are they updated?
> Take for example hgu133a.db and hgu133plus2.db.  I'm using versions  
> 2.2.11
> for both of them.
> With the hgu133plus2.db,
> mget('206902_s_at', env=hgu133plus2ENTREZID)
> returns 9941 as the Entrez ID
> However,
> mget('206902_s_at', env=hgu133aENTREZID)
> returns NA, whereas on the Affymetrix website, the probe set id  
> returns 9941
> as the Entrez ID
> Does this imply that the hgu133a.db package is out of date?
> Thanks,
> Andrew
> 	[[alternative HTML version deleted]]
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