[BioC] Affymetrix gtype_cel_to_pq

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Wed Oct 19 03:00:27 CEST 2005

Basically the Fusion SDK (which is the File SDK mentioned below) is  
implemented through the affxparser package.

It works on Mac OS, Linux'es but currently not on Solaris and  
Windows. The problem seems to be tied to low-level differences in the  
standard libraries. We are working with the people from affy to  
resolve these issues.

But as I said, if Linux/MacOS is ok for you, you are good to go.


On Oct 18, 2005, at 2:25 AM, Henrik Bengtsson wrote:

> Hi,
> I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the
> RLMM package.  This is an non-supported tool by Affy and therefore I
> hope someone else can help me out.
> Affymetrix provides the (platform independent) C++ source code at
> http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and
> says "This is the source code for the gtype_to_cel_pq tool. To build
> this application you will also need to download and compile the File
> SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source
> code provided has only been compiled and tested on a Linux system
> using the g++ version 3.3 compiler.".
> Has anyone successfully built this tool on Unix, Linux or even Windows
> (Cygwin?) and if so could you please tell me what compile and link
> options you used for g++?
> I am aware of Nusrat Rabbee's pre-compile Linux version at
> www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html, but it does not
> run on the Unix system I have access.
> Best wishes
> Henrik Bengtsson
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