[BioC] annaffy annotation problem (hgu133plus2)
Dipl.-Ing. Johannes Rainer
johannes.rainer at tugraz.at
Mon Apr 4 15:59:13 CEST 2005
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?
Quoting Steffen Durinck <sdurinck at ebi.ac.uk>:
> 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":
>  "208078_s_at"
> Slot "table":
>  "SNF1LK"
>  "Probable serine/threonine-protein kinase SNF1LK (EC 22.214.171.124).
>  "q22.3"
>  "21"
>  43658828
>  43671436
>  "ENSG00000142178"
> Dipl.-Ing. Johannes Rainer wrote:
>> 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
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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