Hello, I have been trying to use maskBAD to assess the differences in Affymetrix probe affinity between two different strains of mice. I have imported the CEL files into an affybatch object, and defined a numerical array separating the two groups of microarray chips. When running maskBAD as follows (allcels is the affybatch, z defines the two groups): exmask<-mask(allcels,ind=z,verbose=FALSE,useExpr=T) I get this error message, and no results object is created: Error in FUN(1:8[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 1) and when trying this: exmask<-mask(allcels,ind=z,verbose=FALSE,useExpr=F) I get this error, and exmask is created with results for only 1600 probes (out of >30000). Error in if (sxy != 0) { : missing value where TRUE/FALSE needed If anyone here can identify the source of this problem, I would be happy to hear. Thank you, Ron Rotkopf