I am currently using Aroma's ASCRMAv2 & Paired PSCBS to do a copy number analysis on Affymetrix GenomeWide SNP Array 6.0 data.  I've run the data through but haven't yet seen a measure of quality that will allow me to remove bad samples.

Using Affy's Genotyping Console, I can get MAPD values, but I wasn't sure if there were values (i.e. MAPD, waviness, etc) created and stored in Aroma processing that I can use.  If not, what do others use to identify bad samples?

Thanks in advance for any help,

Gaius