[BioC] affy v codelink

[Dick Beyer]

Hi Binita,

I have done comparisons of affy and codelink.  I used limma on both.  I used no background adjustment for codelink and quantile normalization.  I then got a common gene list from TIGR's Resourcerer:

http://www.tigr.org/tigr-scripts/magic/r1.pl

Good luck,
Dick
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Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
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Message: 17
Date: Thu, 28 Oct 2004 10:42:52 +0200
From: Binita Dutta <binita.dutta at vib.be>
Subject: [BioC] Comparison of Affymetrix and CodeLink chip
To: bioconductor at stat.math.ethz.ch
Message-ID: <6.0.0.22.1.20041028104202.01ebd468 at 194.78.28.203>
Content-Type: text/plain; charset="us-ascii"; format=flowed

Dear All,

I have been using limma for data analysis of affymetrix chips. We want to 
compare result of affymetrix chip and Amersham Codelink. We have done 
experiment with three knock out mice  and compared with the wild type mice. 
Can you suggest us the best bioconductor packages which can be used 
to  fish out differentially experessed genes with P. values on affymetrix 
and codelink slides.


Help in this regard will be highly appreciated.

Binita
==============================

Binita Dutta, PhD
MicroArray Facility(MAF)
UZ Gasthuisberg
Onderwijs en Navorsing
Herestraat 49
3000 Leuven
Belgium