[BioC] how to fastest go from Affymetrix HGU-133 Plus 2.0 chip tiff files to cel files?

Henrik Bengtsson hb at stat.berkeley.edu
Sun Aug 10 18:51:19 CEST 2008

Hi Johan,

On Fri, Aug 8, 2008 at 8:26 AM, Johan Lindberg <johanl at biotech.kth.se> wrote:
> Dear all, I got Affymetrix HGU-133 Plus 2.0 chip tiff-files from a
> colleague, but since I want cel-files to load into R how do I extract
> the probe intensities in the least tedious way?

Answer to the subject line: have the person(s) who scanned the array
to also process it through the Affymetrix image analysis software.
I'm quite sure that if you can scan the array then you also have
access to their image analysis. That will give you CEL files and is
definitely the fastest way to do it.  You don't want to have to deal
with the image files (unless you really think you have a new method
hat improves the probe signal estimates).

> Should I download the software suite from affymetrix or is there some
> faster way to do this?

I am not aware of Affymetrix software that does this and that you can
download for free.  I believe it comes as a bundle with the scanner or



> best regards,
> // Johan
>        [[alternative HTML version deleted]]
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