Dear all, I'm currently playing around with different normalisation methods for a set of arrays without MM probes (Mouse Gene 1.0 ST). I wanted to try gcrma with a set of user-defined background probes, i.e. using the option gcrma(...., NCprobes=mylistofnegativecontrols, type="affinity", ...) Unfortunately I run into problems in the sub-function gcrma.engine2: Error in switch(algorithm, Turlach = { : NA/NaN/Inf in foreign function call (arg 3) > traceback() 8: .C(R_Trunmed, n, k, as.double(x), rmed = double(n), tmp1 = integer(k + 1), tmp2 = integer(2 * k + 1), tmp3 = double(2 * k + 1), as.integer(iend), as.integer(print.level), DUP = FALSE) 7: switch(algorithm, Turlach = { .C(R_Trunmed, n, k, as.double(x), rmed = double(n), tmp1 = integer(k + 1), tmp2 = integer(2 * k + 1), tmp3 = double(2 * k + 1), as.integer(iend), as.integer(print.level), DUP = FALSE)$rmed }, Stuetzle = { .C(R_Srunmed, as.double(x), smo = double(n), n, k, as.integer(iend), debug = (print.level > 0), DUP = FALSE)$smo }) 6: runmed(x[O], 21) 5: bg.parameters.ns(ncs, anc, apm) 4: bg.adjust.affinities(pms[, i], ncs = intensity(object)[NCprobe, i], apm = pm.affinities[, i], anc = intensityaffinity.info)[, i], index.affinities, k = k, fast = fast, nomm = TRUE) 3: gcrma.engine2(object, pmIndex, mmIndex, NCprobe = NCprobe, affinity.info, 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(raw[, 1:2], type = "affinities", affinity.source = "local", NCprobe = background.probes) However, it works if I change the gcrma.engine2 lines: if (type == "affinities") { if (is.null(NCprobe)) pms[, i] <- bg.adjust.affinities(pms[, i], ncs = mms[, i], apm = pm.affinities[, i], anc = mm.affinities[, i], index.affinities, k = k, fast = fast) else pms[, i] <- bg.adjust.affinities(pms[, i], ncs = intensity(object)[NCprobe, i], apm = pm.affinities[, i], anc = intensityaffinity.info)[, i], index.affinities, k = 1, fast = fast, nomm = TRUE) if (GSB.adjust) pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, aff = pm.affinities, fit1 = fit1, k = k) } to: if (type == "affinities") { if (is.null(NCprobe)) pms[, i] <- bg.adjust.affinities(pms[, i], ncs = mms[, i], apm = pm.affinities[, i], anc = mm.affinities[, i], index.affinities, k = k, fast = fast) else pms[, i] <- bg.adjust.affinities(pms[, i], ncs = intensity(object)[NCprobe, i], apm = pm.affinities[, i], anc = intensityaffinity.info)[NCprobe, # added NCprobe subscript here for anc i], index.affinities, k = 1, fast = fast, nomm = TRUE) if (GSB.adjust) pms[, i] <- GSB.adj(Yin = pms[, i], subset = index.affinities, aff = pm.affinities, fit1 = fit1, k = k) } Is the "NCprobe" supposed to be there, or am I missing something here? I can't swear that my list of NCprobes isn't slightly messed up, although I've looked through it and it's been working fine up until this point. Thanks \Heidi > sessionInfo() R version 2.7.0 Patched (2008-05-18 r45723) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.14.1 mogene10stv1cdf_1.18.0 gcrma_2.12.0 matchprobes_1.12.0 [5] affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1 ------------<<>>------------ Heidi Dvinge EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD Mail: heidi at ebi.ac.uk Phone: +44 (0) 1223 494 444 ------------<<>>------------