[BioC] BAF and logR for Affymetrix SNP-arrays

Henrik Bengtsson hb at stat.berkeley.edu
Wed Sep 22 07:59:06 CEST 2010

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.


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
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