[BioC] a problem with Metadat package: hgu133a2

[Shi, Tao]

Hi Ting-Yuan,

Sorry for my forgetfulness.  I was thinking about providing the package version information before
I sent the email out, but still forgot it.

Anyway, here are the information you need:

> sessionInfo()
R version 2.1.1, 2005-06-20, i386-pc-mingw32 

attached base packages:
[1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"    
[8] "datasets"  "base"     

other attached packages:
hgu133plus2        KEGG    hgu95av2     GOstats    multtest  genefilter    survival 
    "1.8.4"     "1.8.1"     "1.8.4"     "1.1.3"     "1.6.0"     "1.6.3"      "2.18" 
     xtable        RBGL    annotate       graph     Biobase       Ruuid     cluster 
    "1.2-5"    "1.3.13"    "1.5.16"     "1.5.9"    "1.5.12"     "1.5.3"    "1.10.1" 
         GO         TSP      hu6800    hgu133a2 
    "1.8.2"       "0.1"     "1.8.4"     "1.8.4" 


I got the NetAffx annotation from the NetAffx analysis center where you can input your probe set
ID and get the annotation interactively.  I've also checked the affy annotation file
("HG-U133A_2_annot.csv") I downloaded on 6/20/05 from this website
(http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133-20).  It has the same
annotation as shown on the NetAffx website now.  I was also suspecting that Affy changed their
annotations after the package was released, until I checked another hgu133a2 annotation file I
have ("HG-U133A_2 gene info.xls", which I downloaded from dChip website on 2/2004).  It's
annotation is also consistent with the current NetAffx anno.

...Tao



--- Ting-Yuan Liu <tliu at fhcrc.org> wrote:

> 
> 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.  
> 
> Best,
> Ting-Yuan
> 
> 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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>