[BioC] annaffy annotation problem (hgu133plus2)

[Dipl.-Ing. Johannes Rainer]

the biomaRt package is very nice,
i also downloaded it and tested it, but as i am behind a (****) http 
proxy i am not able to connect to the according servers at ensembl. i 
assume the package connects directly through a SQL connection to the 
database... would it be possible to use a web service?

cheers, jo

Quoting Steffen Durinck <sdurinck at ebi.ac.uk>:

> Hi,
>
> You could also try using the biomaRt package (see developmental 
> packages).  biomaRt uses direct queries to the latest release of 
> Ensembl to get annotation information.  Ensembl does an independent 
> mapping of the affy probe sequences to the genome sequences.  This is 
> what I got for your affy id:
>
> > library(biomaRt)
> > mart<-martConnect()
> -  Connected to ensembl_mart_29, ensembl_mart_29, ensembl_mart_29 and 
> ensembl_mart_29 -
> > getGene(id="208078_s_at",array="hgu133plus2",mart=mart)
> An object of class "martTable"
> Slot "id":
> [1] "208078_s_at"
>
> Slot "table":
> $symbol
> [1] "SNF1LK"
>
> $description
> [1] "Probable serine/threonine-protein kinase SNF1LK (EC 2.7.1.37). 
> [Source:Uniprot/SWISSPROT;Acc:P57059]"
>
> $band
> [1] "q22.3"
>
> $chromosome
> [1] "21"
>
> $start
> [1] 43658828
>
> $end
> [1] 43671436
>
> $martID
> [1] "ENSG00000142178"
>
>
> Cheers,
> Steffen
>
> Dipl.-Ing. Johannes Rainer wrote:
>
>> hi,
>>
>> i am wondering how the annotation of the Affymetrix chips are 
>> done... i know how the AnnBuilder package works and i also used it, 
>> but as the starting point for any annotation is the GenBank id for 
>> which the probe set codes i would like to know from where this 
>> mapping information comes. are those packages built using the probe 
>> set to genbank mapping that can be downloaded from affymetrix, or 
>> the (sometimes) newer annotation that is available through 
>> Affymetrix NetAffx or some other source?
>>
>> I am really interested in this, because we got a little annotation 
>> problem with the annotation for the hgu133plus2 chip (version 
>> 1.7.0). one of our interesting genes in our study was the probe set 
>> 208078_s_at which is mapped using the hgu133plus2 package (and the 
>> annotation from Affymetrix) to NM_030751 (TCF8). we made real time 
>> PCR to confirm its regulation but this TCF8 was not regulated at 
>> all. so i went back to NetAffx tool and saw that Affymetrix gave a 
>> new annotation for this probe set, all 11 probes perfectly match 
>> with the gene NM_173354 (SNF1LK) (i wonder how Affymetrix could 
>> annotate this gene to the TCF8 gene).
>>
>> if the annotation packages are built using the downloadable probe 
>> set to genbank mapping files from Affymetrix (which may never 
>> updated and corrected for errors by Affymetrix) i believe that there 
>> may be more annotation errors in this package like the one we found.
>>
>> cheers, jo
>>
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>
>