[BioC] annotation on mouse4302

[Steffen]

Hi Mayte,

Adding a third source, Ensembl (which does an independent mapping of the 
affy probes) gives:

 >library(biomaRt)
Loading required package: RCurl
 > ensembl=useMart("ensembl", dataset="mmusculus_gene_ensembl")
Checking attributes and filters ... ok
 > getBM(c("affy_mouse430_2","entrezgene","markersymbol","refseq_dna"), 
filters="affy_mouse430_2", values="1442021_at", mart=ensembl)
 
affy_mouse430_2 entrezgene markersymbol refseq_dna
1      1442021_at      14680         Gnal  NM_177137


So it looks like Ensembl supports the Affy annotation. 
Possibly the difference with the BioC annotation packages is due to 
older annotation versions in BioC.  On October 5th, there is a new 
release of Bioconductor and I assume the annotation packages will be 
updated at that time as well.

Cheers,
Steffen

Mayte Suarez-Farinas wrote:
> Hi
>
> I am using mouse4302 chips and my biology counterpart found some odds  
> annotations,
> for a non negligible number of gene the symbols produced by  
> Bioconductor and affymetrix web  site
> are very different (meaning they are even not synonyms), usually what  
> it happens is that
> the genes are next to each other in the genome (If you look at them  
> in USCS genome browser)
> An example
> probeset: 1442021_at:
>
> Bioconductor annotation
> entrez id: 225651        symbol:Mppe1
> refseq: NM_172630    NP_766218    XM_001001173 XM_001001180  
> XM_001001193 XM_001001206 XM_001001219 XP_001001173
>   XP_001001180 XP_001001193 XP_001001206 XP_001001219
>
> Affy annotation
> entrez id:  14680          symbol: Gnal
> refseq: NM_010307 NM_177137
>
> I guess my question is how is the mapping done, so that it results in  
> such a difference...and which one
> is better. For what reason are those annotation at odds with  
> affymetrix. Which at should believe better ?
>
>
> Thanks in advance
>
> Mayte
>
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