microarray normalization with frma and annotation with custom cdf

Question

[chen xiao]

I plan to normalize the data with frma and annotate the probe sets with a custom cdf.

However, the probe sets in mouse 4302frmavecs is calculated under mouse4302cdf which is consisted of 495374 probes and the custom cdf consisted of about 290000 probes is made based on the current genome annotation data which means that some original probes in 4302cdf was not included in the custom cdf. this means the parameters calculated based on original probes may not appropriate for the new probe sets. So, my question is how you deal with this problem in your paper? Whether I can annotate my probes with a custom cdf for mouse genome 430 2.0 before a frma normalization procedure like this:

>affydata<-ReadAffy(,cdfname="Mouse4302_Mm_ENTREZG")
>eset<-frma(affydata)

Thanks!