Hi , I am traying to calculare the intensity measure for the U133A latinsquare experiment from affymetrix. I am using R 1.8.1 with gcrma version 1.0.0 on linux RedHat 9.0 P4 2.6 GHz, 1Gb Ram I used the following commands: > library(affy) > library(gcrma) > data<-ReadAffy() > data.invariant.gcrma<-gcrma(data, normalize.method="invariantset") and I got the following error and warnings: Loading required package: hgu133atagprobe Loading required package: matchprobes background correction: gcrma normalization: invariantset PM/MM correction : pmonly expression values: medianpolish background correcting...Error in if (!(lo <- min(hi, IQR(x)/1.34))) (lo <- hi) || (lo <- abs(x[1])) || : missing value where TRUE/FALSE needed In addition: There were 50 or more warnings (use warnings() to see the first 50) Warning messages: 1: multi-argument returns are deprecated in: return(y = yhat, wt) .. 50: multi-argument returns are deprecated in: return(y = yhat, wt) Does any body have any suggestion on how to get through this error message? Which is the meaning of the warning messages? Raf -- Prof. Raffaele A. Calogero Genomics and Bioinformatics Unit Dipartimento di Scienze Cliniche e Biologiche c/o Az. Ospedaliera S. Luigi Regione Gonzole 10, Orbassano 10043 Torino tel. ++39 0116705410 Lab. ++39 0116705408 Fax ++39 0119038639 e-fax ++39 0112365410 Mobile ++39 3333827080 email: raffaele.calogero@unito.it www: www.bioinformatica.unito.it _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex