Dear list, I have combined two AffyBatches with the function combineAffyBatch of the matchprobes package. 10 samples were hybridized to hgu133plus2 chips and 15 to hgu133a chips. Now I would like to compute MAS5 expression values for the combined AffyBatch. However, a call to the function mas5 of the affy package produces an error: > ab.comb AffyBatch object size of arrays=0x0 features (94474 kb) cdf=combcdf (22280 affyids) number of samples=25 number of genes=22280 annotation= > mas5(ab.comb) background correction: mas PM/MM correction : mas expression values: mas background correcting...Error in as.vector(data) : NAs in foreign function call (arg 2) In addition: Warning message: NAs introduced by coercion The problem seems to be that the combined AffyBatch has no dimensions and therefore the lines allx <- c(pm.index, mm.index)%%nrow(object) allx[allx == 0] <- rows ally <- c(pm.index, mm.index)%/%nrow(object) + 1 in the function bg.correct.mas of affy produce NaN for allx. Is there a way to circumvent this, e.g. give (virtual) dimensions to the combined AffyBatch? I'm aware that the how-can-I-get-MAS5-expression-values-with-combined- AffyBatches question has already been asked, however I couldn't find a solution in the mailing list archive. Is there one? Thanks Lewin