I currently downloaded a number of SNP datasets from GEO (CCLE)
Also I downloaded Genomewide affymetrix 6.0 SNP array annotation data from affymetrix site.
I imported the SNP 6.0 CEL files using affy package's ReadAffy.
Strangely, every CEL files has approximately 7,000,000 rows but affymetrix annotation data has around 900,000 rows.
What is right way to match probes?