This user manual explains how to import, process, and analyze data from Affymetrix GeneChip Targeted Genotyping arrays, generate genotypes, and manage projects.
The guide provides step‑by‑step instructions for using the Affymetrix GeneChip® Targeted Genotyping Analysis Software, including importing .dat/.cel files, running the analysis workflow, and exporting genotype results. It also describes the software’s project and sample tracking features, quality‑control metrics, and how to customize tables and charts.
Additional chapters cover compatibility modes (GCOS/AGCC), data storage recommendations, server‑maintenance tasks, and troubleshooting procedures for experiment failures, cluster genotyping issues, and file‑location problems. The document is intended for researchers who routinely process array data and need to ensure high‑quality genotype calls.
| Software version | 1.6 |
|---|---|
| Supported scanner | GeneChip Scanner 3000 7G 4C |
| License type | Non‑exclusive, non‑transferable, non‑sub‑licensable |
When a .dat file is created, AGCC or GCOS automatically converts it into a .cel intensity file.
The software works with the Affymetrix GeneChip® Scanner 3000 7G 4C.
Use the Delete Project function described in Chapter 5, page 68.
Affymetrix grants a non‑exclusive, non‑transferable, non‑sub‑licensable license to use the product according to the manual.