Affymetrix understands that a microarray experiment doesn't end at the lab bench. In fact, that's when the real work is just beginning. To get you quickly down the road to publication, Affymetrix provides highly flexible genotyping and copy number analysis solutions: standalone Genotyping Console software; cross-platform, command-line applications available through Affymetrix Power Tools (APT); and a network of GeneChip®-Compatible™ providers for advanced statistical analysis.

Download Information and Instructions
	Download Genotyping Console 2.1

Genotyping Analysis
Genotyping Console streamlines whole-genome genotyping analysis and quality control. Genotyping Console implements robust genotyping algorithms—including Birdseed for SNP Array 6.0, BRLMM-P for the SNP Array 5.0 and BRLMM for the 500K Array—as well as cluster visualization (Figure 1) and flexible SNP filtering capabilities (Figure 2).

Researchers can generate per-SNP cluster graphs as well as pdf reports for batch analysis.

Figure 1	Figure 2
		Figure 1 : SNP Array 6.0 genotype cluster Figure 2 : Flexible SNP filtering capabilities

New! Copy Number and LOH Analysis
Genotyping Console now includes copy number and LOH algorithms for the SNP Array 6.0 as well as new Genotyping Console Browser and Segment Reporting Tool. Genotyping Console also incorporates CNAT 4.0 copy number and LOH algorithms for the GeneChip® 250K and 500K Arrays.

Figure 3
	Figure 3 : An example of a polymorphic CNV in two HapMap samples displayed in the GTC Browser's Chromosome View.

Take a tour of the key features in Genotyping Console for CNV analysis in association studies.

Take a tour of the key features in Genotyping Console for cytogenetic studies.

For a full-featured solution for copy number analysis in cancer studies, we recommend Partek® Genomics Suite™. Take a tour of the key features in Partek GS for cancer copy number studies.