[BioC] a problem with Metadat package: hgu133a2

Ting-Yuan Liu tliu at fhcrc.org
Wed Oct 5 01:05:02 CEST 2005

Hi Tao,

ChenWei is not the current maintainer for the meta data packages, but I 
will try to figure what's wrong here for him.

Could you provide the result of sessionInfo()?  People can get more 
information about the versions of the packages you are using and then will 
be easier to determine the source of problem you have.  

Also, could you tell me which file did you get from NetAffx?  When was 
this file release?  Affymetrix released their annotation files at least 
twice after our last release on May.  If you are comparing the package of 
BioC 1.6 with the file you recently downloaded, you might find that there 
are some inconsistent because Affymetrix updated the file.   

Any way, please provide the information I mentioned above so that I can 
determine if you were in such a inconsistent situation.  


On Tue, 4 Oct 2005, Shi, Tao wrote:

> Hi Chenwei,
> I ran into this problem totally by random.  The annotation for this particular probeset is
> diffrent from what I got from NetAffx:
> > version
>          _              
> platform i386-pc-mingw32
> arch     i386           
> os       mingw32        
> system   i386, mingw32  
> status                  
> major    2              
> minor    1.1            
> year     2005           
> month    06             
> day      20             
> language R              
> > get("221770_at", hgu133a2GENENAME)
> [1] "solute carrier family 4, sodium bicarbonate transporter-like, member 10"
> which should be for "206830_at".
> > get("206830_at", hgu133a2GENENAME)
> [1] "solute carrier family 4, sodium bicarbonate transporter-like, member 10"
> The annotation I got from NetAffx is:
> 221770_at   ribulose-5-phosphate-3-epimerase
> Could you please check what's going on?  Thanks,
> ...Tao
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