library(affy)
library(frma)
install.packages("hgu133plus2hsentrezgcdf_15.0.0.tar.gz", repos=NULL, type="source")
data <- ReadAffy(cdfname="HGU133Plus2_Hs_ENTREZG")
object <- frma(data)
Error in frmaAffyBatch(object, background, normalize, summarize, input.vecs,  :
  Mismatch between pmindex(object) and names of input.vecs and unable to create unique mapping.

It's been a long time since I processed array data and I could really do with some advise for resolving this error.

The frozen RMA estimates for that array are based on the conventional probe -> probeset mappings, not the MBNI re-mapped probeset definitions. If you want to use frma, you need to use the conventional cdf.

There are frozen parameters for one alternative probe mapping. To find out the alternative CDF version that is currently available, you can do the following:

library(hgu133plus2frmavecs)
data(hgu133plus2hsentrezgfrmavecs)
hgu133plus2hsentrezgfrmavecs$version

It looks like you were using hgu133plus2hsentrezgcdf_15.0.0 when the alternative CDF version that matches the current frmavecs is hgu133plus2hsentrezgcdf_19.0.0.

Hope that helps.