Unfortunately, I'm running into the same problems and haven't been able to apply the fRMA method to a number of Affymetrix genechips, including Mouse Genome 430A 2.0, Mouse Exon 1.0 ST Array, MOE430A, and MOE430B. When I try install the necessary packages I continue to get the following warning "package ‘XXX’ is not available (for R version 3.3.1)".
I have tried installing older versions of R but this hasn't helped.
Is there anyway aroudn this? Thank you in advance for your help!