[BioC] annaffy annotation problem (hgu133plus2)

[Dipl.-Ing. Johannes Rainer]

great!!! this sounds nice, the only thing that i will have to update 
the local BioMart database frequently :( .

Quoting sdurinck at ebi.ac.uk:

> Hi Jo,
>
> You could do a local install of the Ensembl biomart database.  Normally
> the latest Ensembl release is downloadable from
> http://www.ebi.ac.uk/BioMart/install.html
> but I am not able to access this right now. If you then change in biomaRt
> the host to your local host you should be able to use it.  You need to do
> this in the package R code but I'll update the package later this week so
> you can do this from within R.
>
> best,
> Steffen
>
>> 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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>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>
>>>
>>
>>
>>
>>
>
>