BAF and logR for Affymetrix SNP-arrays
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@alla-bulashevska-3873
Last seen 10.3 years ago
Dear Bioconductor users, I would like to use SOMATICS R script (heterogeneous tissue analysis) written for the analysis of Illumina SNP-arrays for my Affymetrix SNP-array data. I need to calculate BAF (B-allele frequency) and logR estimates which are normally outputed from Illumina BeadStudio software. My question is, if there exist an R package which calculates this values from Affymetrix CEl-files and if this will be valid to use these values in SOMATICS or other packages written for Illumina data. Thank you in Advance, Alla Bulashevska
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@henrik-bengtsson-4333
Last seen 7 months ago
United States
The aroma.affymetrix package can process nearly all Affymetrix CN & SNP arrays and can provide you with estimates of total copy-number for all loci and allele B fractions for all (bi-allelic) SNPs. For more details and further discussion, go to http://www.aroma-project.org/. I let someone else answer your question if it is sensible to pass that on to SOMATICs. /Henrik On Mon, Sep 20, 2010 at 12:42 PM, Alla Bulashevska <alla.bullashevska at="" fdm.uni-freiburg.de=""> wrote: > > Dear Bioconductor users, > I would like to use SOMATICS R script (heterogeneous tissue > analysis) written for the analysis of Illumina SNP-arrays > for my Affymetrix SNP-array data. I need to calculate BAF > (B-allele frequency) and logR estimates which are normally > outputed from Illumina BeadStudio software. My question is, > if there exist an R package which calculates this values > from Affymetrix CEl-files and if this will be valid to use > these values in SOMATICS or other packages written for > Illumina data. > Thank you in Advance, > Alla Bulashevska > > _______________________________________________ > 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 >
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