[BioC] affy 10k

[Benilton Carvalho]

Unfortunately, that won't be sufficient (not for genotyping).

One reason is that 10k is not in wide use indeed. But, also, to the  
best of our knowledge, there is not training data on that platform  
(HapMap samples and genotype calls), which would allow us to estimate  
the parameters needed by CRLMM.

b

On Nov 2, 2009, at 2:57 PM, Vincent Carey 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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>
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