[BioC] annotation on mouse4302

[Marc Carlson]

Steffen wrote:
> 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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>>
>>
>>     
>
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>
>   
Hi guys.

It looks like the information at Affy has been updated since March. 
This is the source that we use to build the latest annotation packages
for each release.   Using the very latest mouse4302.db package from our
devel branch, I get the very same answer as the ensemble folks above. 
Whereas if I use the older annotations from last March, I get "Mppe1"
instead.  So it looks like you might want to consider updating
annotation packages soon.  The new stuff will be in release on the 5th,
but you can get it now from devel  right now if you feel adventurous.


Here is the code I ran:

library("mouse4302.db")
ls(2)

get("1442021_at", env=mouse4302SYMBOL)

# this gets me:  [1] "Gnal"


get("1442021_at", env=mouse4302GENENAME)

# and this gets me:  [1] "guanine nucleotide binding protein, alpha
stimulating, olfactory type"



#And my sessionInfo() (in case you want to know):
R version 2.6.0 alpha (2007-09-13 r42838)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

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

other attached packages:
[1] mouse4302.db_1.99.3  AnnotationDbi_0.99.8 RSQLite_0.6-0
[4] DBI_0.2-3            Biobase_1.15.36

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15


    Hope this helps,

        Marc