Hello all, I would like to use spikein and HGU-133ATAG experiment for Concentrations comparison. The relationship between Spikein and HGU-133ATAG is still unclear to me. I have a small program, which runs with SpikeIn in affy Package without errors: data(SpikeIn) pms <- pm(SpikeIn) mms <- mm(SpikeIn) concentrations <- matrix(as.numeric(sampleNames(SpikeIn)), 20, 12, byrow = TRUE) par(mfrow = c(1, 2)) matplot(concentrations, pms, log = "xy", main = "PM", ylim = c(30,20000)) lines(concentrations[1, ], apply(pms, 2, mean), lwd = 3) matplot(concentrations, mms, log = "xy", main = "MM", ylim = c(30,20000)) lines(concentrations[1, ], apply(mms, 2, mean), lwd = 3) Now I would like to run same test with Hg-U133ATAG. My algorithm has 5 steps: A. READ *.CEL file --> data.raw (AffyBatch Object) B. extract probe sets from AffyBatch Object --> pset C. INIT. PM and MM from pset D. Calculate Concentrations (if NA THEN pset = pset[!is.na(pset) ]) E. matplot for PM and MM afterwards I write in R: # Upto 42 Experiments: library(affy) data.raw <- ReadAffy(filenames="H:/Profile/Eigene Dateien/Dip_bak/Pr_sprach/R/ME_cel/Expt1_R1.CEL") ps <- probeset(data.raw) pms <- pm(ps[[1]]) mms <- mm(ps[[1]]) #concentrations <- matrix(as.numeric(sampleNames(ps[[1]])), 20, 1, byrow = TRUE) #Warning message: #NAs introduced by coercion psna = ps[[1]][!is.na(ps[[1]])] concentrations <- matrix(as.numeric(sampleNames(ps[[1]])), 16, 1, byrow = TRUE) # No Answer!? I cannot find my source of error. Can Someone help me? Thanks, Mohammad Esad-Djou