[BioC] affy 10k

[Vincent Carey]

It has been pointed out to me that the main genotyping facilities for
snp chips in bioconductor require availability of hapmap samples for
calibration.  As far as I know, the 10k chip was not applied to hapmap
data, so neither snprma nor crlmm can work for this platform.

On Mon, Nov 2, 2009 at 11:57 AM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> My recollection is that we did not build for this chip because it was
> not in wide use.  You should be able to build a pd.mapping* package
> using the pdInfoBuilder package.
>
> On Mon, Nov 2, 2009 at 9:22 AM, Peter Robinson
> <peter.robinson at charite.de> wrote:
>> Dear Listers,
>>
>> I would like to use the oligo package to do genotype calls for the
>> affymetrix 10K chip. For some reason, I have not been able to find a package
>> like "pd.mapping250k.sty", which is used for the 250K/Sty chip.
>>
>> In other words, I had used this code for the 250k chip:
>>
>>>biocLite("pd.mapping250k.sty")
>>
>>
>>
>>>library("oligo")
>>>outputDir <- file.path(getwd(), "myGenotype")
>>>fullFilenames <- list.files("myDirectory",pattern="CEL$",
>>> ignore.case="TRUE",full.names=TRUE)
>> crlmm(fullFilenames, outputDir, verbose = TRUE)
>>
>>
>> and I am not sure what annotation file to use for the 10K (if in fact there
>> is one). Thanks for any tips!
>> -Peter
>>
>>
>> --
>> Dr. med. Peter N. Robinson, MSc.
>> Institut für Medizinische Genetik
>> Universitätsklinikum Charite
>> Humboldt-Universität
>> Augustenburger Platz 1
>> 13353 Berlin
>> Germany
>> voice: 49-30-450569124
>> fax:   49-30-450569915
>> email: peter.robinson at charite.de
>> http://compbio.charite.de/
>> http://www.human-phenotype-ontology.org
>>
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>