[BioC] Problems with mas5calls for ygs98 chips

[Jarno Tuimala]

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