I've been trying to calculate P/A/M calls for Affymetrix yeast (ygs98) chips, but failed. The script I've used works fine for human and mouse chips. Could somebody suggest how to resolve this? The R I'm using is 2.2.1 and Bioconductor packages are from release 1.7. The same problem seems to appear in both Linux and Windows versions. I've tried some CEL-files produced by my collegues, and even the Affymetrix demo files from http://www.affymetrix.com/support/technical/sample_data/demo_data.affx , but they both give the same error message. However, calculation of intensity values succeeds. Here are the commands and messages generated by R: > library(affy) > library(ygs98) > library(ygs98cdf) > library(ygs98probe) > dir() [1] "Yeast-1-121502.CEL" "Yeast-2-121502.CEL" > d<-ReadAffy() > data.mas5<-mas5(d) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 9335 ids to be processed | | |####################| > calls<-mas5calls(d) Getting probe level data... Computing p-values Making P/M/A Calls Error in if (y < alpha1) { : missing value where TRUE/FALSE needed Best Regards, Jarno Tuimala Finland