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Remapped CDF Web Server Software

How to use our remapped CDF files with
Affymetrix GCOS, dCHIP, or BioConductor

  • Remapped CDFs based on GenBank and RefSeq can be downloaded from the Remapped CDF webpage
  • Remapped CDFs based on RefSeq can be generated on the Web Server webpage

Affymetrix GCOS software (Windows only)

  • Download Affymetrix CCDS (or RefSeq) GCOS distribution from Remapped CDF
  • Unzip and unpack the distribution
  • Replace the three files CDF, PSI, and GIN in the GCOS library distribution
  • Re-install the library
As an example, for the transcript-consistent analysis of the HG-U133A chip
  • Download the remapped GCOS distribution by choosing "HG-U133A CCDS (or RefSeq) GCOS" on the Remapped CDF webpage
  • Unzip and unpack the distribution
  • Download the library package "hgu133_libraryfile" from the Affymetrix web site
  • Unzip and unpack the downloaded library package
  • Replace the three files "HG-U133A.psi," "HG-U133A.cdf," and "HG-U133A.gin" in the library package "hgu133_libraryfile" (in the subdirectory "CD_HG-U133\Full\HG-U133A\LibFiles") with the corresponding remapped files
  • Click "Setup.exe" (in the subdirectory "CD_HG-U133\Full") to re-install the library

dCHIP (Windows only)

  • Download Affymetrix CCDS or RefSeq GCOS distribution from Remapped CDF webpage
  • Unzip and unpack the distribution
  • Use the CDF file in dCHIP just as the way that uses Affymetrix CDF files (refer to dCHIP webpage for more information)

BioConductor (Windows, Linux/Unix)

  • Download the remapped CDF R package from the Remapped CDF webpage
  • Install the package in the R environment
    • Under Windows
      • Invoke R
      • Select menu "Packages->Install package(s) from local zip files"
    • Under Linux/Unix
      • Type "R CMD INSTALL *.tar.gz".
  • Type one line of R code (see specific examples below) in the script to modify the value corresponding to "cdfName" for AffyBatch to use the remapped CDF
  • Load annotations which include the following data (OPROBE, SYMBOL, ACCNUM, ENTREZGENEID, probeinfo, annotinfo)
As an example, for the transcript-consistent analysis of the HG-U133A chip under Linux/Unix
  • Download the remapped CDF and the corresponding annotation on the Remapped CDF webpage
  • Install the package in the R environment under Linux/Unix
  • Type "R CMD INSTALL hgu133atranscriptccdscdf_1.8.0.tar.gz"
    "R CMD INSTALL hgu133atranscriptccds_1.1.0.tar.gz"
  • Type one line of R code as shown in the following context
      library(hgu133atranscriptccds);
      data<-ReadAffy();
      data@cdfName<-"hgu133atranscriptalt"
      for(f in dir(file.path(.path.package("hgu133atranscriptccds"),"data"), pattern=".rda",full.names=TRUE)) load(f)
      ls()

AffyProbeMiner is a joint development of the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR) National Cancer Institute (NCI) and Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center. If you have any problems, questions or feedback on the tool, please email us.

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