Unable to get genotypes for all markers

[chopraamhk]

Dear Dr. Wang,

I am trying to work on CNV using PennCNV-affy. I have generated summary.txt and report.txt for Axiom PMRA Array using APT genotype axiom. Further i am generating genotype cluster and i am getting half number of genotype (~4 lakhs) out of around (~9 lakhs probesets).

WARNING: A total of 26341 markers do not have chromosome annotation in locfile GWAS.map and were skipped
WARNING: A total of 439252 markers do not have at least two types of genotypes (out of AA, AB, BB) and were skipped
NOTICE: A total of 436967 SNP markers have been analyzed to construct canonical clustering positions
NOTICE: A total of 0 CN markers have been analyzed to construct canonical clustering positions

Could you please guide me why am i not getting genotype for all and why am i getting this warning?

Thank you!

Best Wishes,
Mehak

[mdcRed]

I'm having exactly same issues, and not sure if there is suggestions of what might have been the issue(s). I also am using Thermofisther Axiom array.