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 f?r Medizinische Genetik >>> Universit?tsklinikum Charite >>> Humboldt-Universit?t >>> 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 >