NASC's Affymetrix Service: Converting CELs

Converting between .CEL file formats.

Many analysis tools (e.g. Genespring, R/Bioconductor) standardly accept all Affymetrix .cel formats. However, several important tools (xspecies, J-express, Dchip) require .CEL files to be in earlier formats (text - v3; or early binary - v4).

Affymetrix has generously provided free tools to allow for conversion between these filetypes:

v4 (pre-2009: xda) to v3 (text)

  • Celconverter exe batch-file processor for use on PC OS only.

    AGCC format (v5 - 'Calvin'; post 2008) to all formats (and back).

  • AGCC powertools suite. Use apt-cel-convert.
    • Requires Affy login registration (free)
    • Available for all OS (e.g. PC, OSX, Linux)
    • Download the powertools package
    • Instructions are in the Docs folder.

      OSX example 1 - to convert all v5 .CEL files in current folder to v3 (text) .CEL files in the subfolder 'done':

      ./apt-cel-convert -f text -o done *.CEL

      OSX example 2 - convert v4 .CEL in current folder called dan.CEL to a v3 .CEL in subfolder 'done':

      ./apt-cel-convert -f text -o done dan.CEL

      OSX example 3 - convert v3 .CEL in current folder called sam.CEL to a v4 .CEL in subfolder 'done':

      ./apt-cel-convert -f xda -o done sam.CEL