Chip types: Mapping250K_Nsp & Mapping250K_Sty

Affymetrix press release: New Affymetrix Microarray Set Genotypes More Than 500,000 SNPs in a Single Experiment; GeneChip Human Mapping 500K Array Set Enables Researchers to Perform Highly Detailed Whole-Genome Association Studies for the First Time, Sept 28, 2005.

The so called 500K SNP chip set, which consists of two chip types Mapping250K_Nsp and Mapping250K_Sty, interrogates 500,568 (=262264+238304) SNPs. The SNPs were select based their technical performance, not based on linkage disequilibrium (LD).

Mapping250K_Nsp

> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mapping250K_Nsp
Filename: Mapping250K_Nsp.cdf
Filesize: 185.45MB
Chip type: Mapping250K_Nsp
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 262338
Cells per unit: 24.98Number of QC units: 6

Mapping250K_Sty

> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Sty")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/Mapping250K_Sty
Filename: Mapping250K_Sty.cdf
Filesize: 175.83MB
Chip type: Mapping250K_Sty
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 238378
Cells per unit: 27.49
Number of QC units: 6

Resources

By aroma-project.org:

• UFL: Mapping250K_Nsp,na31,HB20101007.ufl.gz & Mapping250K_Sty,na31,HB20101007.ufl.gz
  Scripts: scripts/Mapping250K_Nsp,UFL,na26.R, scripts/Mapping250K_Sty,UFL,na26.R.
• UGP: Mapping250K_Nsp,na31,HB20101007.ugp.gz & Mapping250K_Sty,na31,HB20101007.ugp.gz
  Scripts: scripts/Mapping250K_Nsp,UGP,na26.R, scripts/Mapping250K_Sty,UGP,na26.R.
• ACS: Mapping250K_Nsp,HB20080710.acs.gz & Mapping250K_Sty,HB20080710.acs.gz

Affymetrix.com:

• Product page: GeneChip Human Mapping 500K Array Set
• Datasheet
• Support Materials (SNP annotation files with SNP positions, dbSNP ID, fragment lengths etc. Probe sequences.)

dChip.org:

• dChip data files: genome information file