[BioC] maskBAD package - Errors during creation of mask

[Ron Rotkopf]

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