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

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 >