[BioC] affy v codelink
Dick Beyer
dbeyer at u.washington.edu
Thu Oct 28 18:02:36 CEST 2004
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
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
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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
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