Custom CDF: HuEx-1_0-st-v2 from Brainarray ENSE and ENSG

Author: Steve Pederson & Henrik Bengtsson
Last updated: 2012-01-29

> cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2", tags="U-ENSG,G-ENSE,v14.1,SP20120129")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,U-ENSG,G-ENSE,v14.1,SP20120129.cdf
Filesize: 45.27MBChip type: HuEx-1_0-st-v2,U-ENSG,G-ENSE,v14.1,SP20120129
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 35202Cells per unit: 186.17
Number of QC units: 0

Downloads:

• HuEx-1_0-st-v2,U-ENSG,G-ENSE,v14.1,SP20120129.cdf.gz - Custom CDF. Contributed by Steve Pederson (School of Mathematical Sciences, The University of Adelaide), January 2012.
• HuEx-1_0-st-v2,U-ENSG,G-ENSE,v.14.1,SP20120129.supportfiles - Contains the probe_tab file & mapping of probes to genomic co-ordinates for genome build GRCh37/hg19.
• The script used to build the above is available at: buildCustomCdf.SP20120129.R

Notes:

• This CDF was created by taking the common probes between v14.1 of the Gene (ENSG) and Exon (ENSE) annotations from Brainarray (U Michigan).
• Probes were placed into 289,999 groups based on common exon mappings.
• Probes were placed into 35,202 units based on gene annotations.
• Every probe maps uniquely to one group.
• Every group maps uniquely to one unit.
• Some groups contain more than 4 probes. For a visual summary see this.