FRMA processing on two different datasets of affy u133A not same dimensions

Question

[jmannhei]

Hi all.

I have the original NCI60 dataset .CEL files that are on affymetrix hg-u133A chips, then I have another data sets that are also on affy u133A chips. When I try to normalize them together with frma I get the following

Error in affyio::read_abatch(filenames, rm.mask, rm.outliers, rm.extra,  : 
  Cel file GSM3239255_UACC-257_vorinostat_1000nM_24h_U133A.CEL does not seem to have the correct dimensions

So I ran frame on the two groups separately and one chip has 22277 probes and the other has 22283 . It looks like the probes are the same with the exception of the extra 6 one has.

In my analysis best practices wold dictate that I would normalize them together but because of this dimensional mismatch I cannot. First, I an not sure why there is a difference since they are both hg-u133A (different generations?). Second is there anyway to get around this?

Thanks