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HsEx10stv2_Hs_REFSEQ

Author: Mark Robinson
Created on: 2008-07-28

Human Exon Array -- "Brainarray" annotation

> cdf <- AffymetrixCdfFile$byChipType("HsEx10stv2_Hs_REFSEQ")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HsEx10stv2_Hs_REFSEQ
Filename: HsEx10stv2_Hs_REFSEQ.cdf
Filesize: 32.16MB
File format: v4 (binary; XDA)
Chip type: HsEx10stv2_Hs_REFSEQ
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 56283
Cells per unit: 116.44
Number of QC units: 0
RAM: 0.00MB

> getUnitNames(cdf)[20789]
[1] "4136241_at"
> getUnitNames(cdf)[20790]
[1] "NM_000014_at"

Notes:

  • The group from Michigan known as "Brainarray" (http://brainarray.mbni.med.umich.edu/) have created a number of "Custom CDF" files for a range of Affymetrix platforms.
  • Above is an example of the REFSEQ probe organization for the Human Exon platform. Many other platforms are available for many organisms.
  • Note that with the 56,283 units for this chip, the first 20,789 are not RefSeqs. I think they are genomic background probes, but I'm not sure.
  • To download one of these for your favourite chip, click on the "Download Custom CDF Files" link from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
  • The file you will want is the <chip_organism_mapping>.cdf which is contained in the zip file under the column "CDF&Seq&Map&Desc". It is an ASCII cdf file, so be sure to use convertCdf() to convert it to binary before using it for processing data.