How to convert binary Affymetrix .CEL files in text format


1. If your CEL file was produced with the GCOS software from Affymetrix:



The .CEL files produced by Affymetrix stations are in a binary form that is only readable by softwares developped by Affymetrix. You probably want to have direct access to your data, and play with them the way YOU want, so you'd love to have them in a text file readable by any routine. Fortunately, the company released a tool to do this convertion.

To do this, install these two files (md5 = e947c4b8eed72610180020ff38f40685) in a directory of a Windows PC computer. Copy your .CEL files in this same directory and double clic on CellFileConversionTool.exe You want to convert format 4 into format 3, so click on this option and press return. After the (long) run, your datafiles are converted in a text format.


Of course you still need the library files telling you what probe (sequence, gene etc...) is located at each (X,Y) coordinate, so you should ask your platform for the library corresponding to your chip.


2.  If your CEL file was produced with the GACC (CommandConsole) software from Affymetrix:


You then need the apt-cel-convert tool which belongs to the Affymetrix Power Tools . The nice thing is the availability of various binaries of this toolbox (and even source code!!!), which make it usable from any platform including Linux.