[BioC] CLF/PGF parser

Kasper Daniel Hansen khansen at stat.Berkeley.EDU
Thu Jun 14 18:10:28 CEST 2007

Hi Jim (with a cc to BioC so other interested parties can take note,  
and a cc to devnet at affy in case there has been any updates).

The strange situation right now is that CLF/PGF files cannot be  
parsed using the Fusion SDK (Affy's official file parsing SDK). There  
are codes for parsing the files somewhere inside the source code of  
the EXACT tools (I think - at least somewhere in the source of one of  
Affy's programs). We are however loathe to take that code and add it  
to affxparser because sooner or later, the SDK ought to start  
supporting CLF/PGF files and then the time spent doing that would be  
more or less wasted. Of course that decision is easier to make when  
none of us have a use for parsing these files at the moment.

I find it somewhat strange that the file format has not been added to  
the official SDK yet (I just checked version 1.09 again and I could  
not find it), and I encourage everyone to mention it to their  
Affymetrix representatives. As soon as that has been done, we will  
start incorporating it into affxparser, something that should be a  
fairly simple task.


On Jun 13, 2007, at 7:49 AM, James MacDonald wrote:

> Hi Kasper,
> Do you have any plans to add parsers for CLF/PGF files to affxparser?
> Best,
> Jim
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> **********************************************************
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