Dear list, I try to run gcrma using the affinity computation without taking into account MM probes i.e. by using the compute.affinities2 function as in if(require(affydata) & require(hgu95av2probe) & require(hgu95av2cdf)){ data(Dilution) ai <- compute.affinities2(cdfName(Dilution)) Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities") } Unfortunately, the above results in > ai <- compute.affinities2(cdfName(Dilution)) Computing affinities.Done. Warning message: xy2i is deprecated and will be removed in the next BioC release. Use xy2indices in the affy package instead. > Dil.expr<-gcrma(Dilution,affinity.info=ai,type="affinities") Adjusting for optical effect....Done. Error in .local(object, ...) : subscript out of bounds > traceback() 6: .local(object, ...) 5: mmaffinity.info) 4: mmaffinity.info) 3: gcrma.engine(pms = pm(object), mms = mm(object), ncs, pm.affinities = pm( affinity.info), mm.affinities = mmaffinity.info), anc, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, verbose = verbose, fast = fast) 2: bg.adjust.gcrma(object, affinity.info = affinity.info, affinity.source = affinity.source, NCprobe = NCprobe, type = type, k = k, stretch = stretch, correction = correction, GSB.adjust = GSB.adjust, rho = rho, optical.correct = optical.correct, verbose = verbose, fast = fast) 1: gcrma(Dilution, affinity.info = ai, type = "affinities") Am I overlooking something which explains the error above ? Many thanks in advance, Marianne P.S. > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hgu95av2cdf_2.3.0 hgu95av2probe_2.3.0 affydata_1.11.5 [4] gcrma_2.14.1 matchprobes_1.14.1 affy_1.20.2 [7] Biobase_2.2.2 JavaGD_0.5-2 rJava_0.6-2 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0 [[alternative HTML version deleted]]