[BioC] affy 10k

[Henrik Bengtsson]

For the record, there are two *different* Affymetrix 10K chips:
Mapping10K_Xba131 and Mapping10K_Xba142.  They are not the same
(physical chip types):

http://groups.google.com/group/aroma-affymetrix/web/mapping10k-xba131
http://groups.google.com/group/aroma-affymetrix/web/mapping10k-xba142

I think dChip do genotyping on both of these, but I might be wrong.

My $.02

/Henrik

On Mon, Nov 2, 2009 at 9:04 AM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>