SNP 6.0 Probe Level Access Tool というのが出てる

SNP 6.0 Probe Level Access Tool (SPLAT) is research tool for customers who are investigating the use of SNP 6.0 for genome-wide copy number. SPLAT extracts probe intensities for collections of Genome-Wide SNP Array 6.0 CEL files. The software tool writes output files that contain normalized probe intensities (not copy number values) and genomic position information in tabular format for more than 1.8 million genetic markers from both SNP and copy number probes on the SNP Array 6.0. Download the SPLAT user manual here.

Affymetrixの新しいMapping array (SNP chip) にはコピー数解析用にSNPのない部分にもプローブを割り当てているようだ*1

*1:SNP 5.0と6.0はそうっぽい