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It is possible to use the functions BAFfromGenotypes and/or getLogRRatio while setting custom Rexpected values?
I am assuming the model at page 10 of the manual (http://bioconductor.org/packages/release/bioc/vignettes/GWASTools/inst/doc/Affymetrix.pdf).
The only option that I found was to change the estimation from plate to the entire study.
