I used a mask file to exclude certain probes in MAS5 to generate the CEL files. After loading the CEL files using the ReadAffy in BioC, the masks slot in the CEL object is empty. Using rm.mask=T didn't change this: > cel@masks <0 x 0 matrix> What's the best way to achieve this (i.e, to exclude some probes before any express calculations) in BioC? Thanks, Xiao-Jun