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Jarno Tuimala
▴
140
@jarno-tuimala-1650
Last seen 10.2 years ago
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