[BioC] plans for binary version of *.CEL files

[Kulp, David]

The details are fairly simple.

Binary formats are being introduced to reduce file size and speed data
access.  Developers have basically two options:

1. Affymetrix sells a developer's license to a linkable library for reading
GeneChip file formats.  (There are also APIs/libraries available for
accessing backend servers.)  Currently Affymetrix provides Windows and java
implementations.  There are no end-user costs or distribution restrictions
on software that is compiled using this library.  Thus, Bioconductor
developers can choose to write to the API or provide a compile-time switch
to do so for those with the Affymetrix library.  Anyone compiling from
source would need a license.  Bioconductor can provide free precompiled
binaries.

2. Affymetrix provides a MAGE-ML exporter (available for download from the
website) which outputs data into an ASCII format that is open and easily
parseable.  It contains all of the "CEL" data you expect.  There is no cost
to use this format.  Because the individual cell data is stored in an
accompanying ASCII file, there is no significant "XML bloat".  

The first option may be the preferred option in terms of speed and long-term
compatibility.  It also is the easiest to use for the end-user because no
conversion is required.  The second option is simple, free, and comparable
to performance of the current ASCII CEL files.

I recommend joining the Affymetrix Developer Network for more information.

David Kulp

-----Original Message-----
From: Warnes, Gregory R [mailto:gregory_r_warnes at groton.pfizer.com] 
Sent: Wednesday, June 25, 2003 7:37 AM
To: 'James MacDonald'; sgh at breastcenter.tmc.edu; ririzarr at jhsph.edu;
rafa at jhu.edu
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] plans for binary version of *.CEL files


I second that.

-G

> -----Original Message-----
> From: James MacDonald [mailto:jmacdon at med.umich.edu]
> Sent: Wednesday, June 25, 2003 10:17 AM
> To: sgh at breastcenter.tmc.edu; ririzarr at jhsph.edu; rafa at jhu.edu
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] plans for binary version of *.CEL files
> 
> 
> All I ever do these days is analyze Affy data, so I am very interested
> in knowing the details. I promise I won't be bored ;-D
> 
> Jim
> 
> 
> 
> James W. MacDonald
> UMCCC Microarray Core Facility
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> ririzarr at jhsph.edu 06/25/03 09:41AM >>>
> there are several 
> alternatives we are considering. i wont bore you with details (unless
> you 
> ask me to). according 
> to affymetrix, ascii cel files will be supproted for one more 
> year. but
> 
> there is a possibility that things will become more difficult for 
> bioconductor  users in the future.  bioconductor is talking to
> affymetrix 
> about this issue. 
> 
> you may want to contact your affymetrix sales rep and explain your 
> situation.
> 
> 
> On Wed, 25 Jun 2003, Susan G. Hilsenbeck wrote:
> 
> > How does, or how will the affy packages in bioconductor handle the
> newer 
> > binary versions of the *.cel files?
> > 
> >
> 
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