pennCNV error "FATAL ERROR:EmGenderCelListener::fillInContrastValues() "

[zhixiang]

I use pennCNV to process the CEL files from affymetrix 6 SNP.

When I run the first step "apt-probeset-genotype", it works for most of the cel files, but for some cel files, the program exited with a fatal error:

"FATAL ERROR:EmGenderCelListener::fillInContrastValues() - Warning. alleleMedian() failed for probeset: SNP_A-8311675"

Can someone help me to figure out this problem?

Thanks

[ncemami]

For future reference, I ran into this same problem (with a different array) when calling the Affymetrix Power Tools "apt-probeset-genotype" v1.6.10 http://www.affymetrix.com/estore/sup...F14CBECCE0D887. The problem was that I was trying to force the genders by invoking the "--read-genders" option, thus bypassing the gender calling methods by explicitly providing sample genders. When I removed this flag and reverted to the "--set-gender-method cn-probe-chrXY-ratio" option, this alleleMedian() error goes away.