[BioC] How to handle 2-channel array that is duplicated on a slide

[James W. MacDonald]

Hi Noah,Noah Cohen wrote:
> Hi - I am a Biioconductor neophyte trying to look at data from a
> 2-channel cDNA microarray that has about 3,000 genes (primarily equine)
> related to inflammatory and immune response that have been read using
> ImaGene software.  The slides are arranged such that the array is
> duplicated on the top and bottom half of the slide (ie, the array of
> genes is printed twice on each slide).  
> 
> Is there somewhere I can read about how to handle such a slide format,
> beginning with exploratory data analysis (such as basic plots) and
> normalization?

I would look at the limma User's Guide. If you have limma installed 
(likely), then

library(limma)
limmaUsersGuide()

will get you started.

Best,

Jim


> 
> Thank you - Noah Cohen
> 
> 
> Noah D. Cohen, VMD, MPH, PhD, DACVIM
> Professor
> Department of Large Animal Clinical Sciences
> College of Veterinary Medicine and Biomedical Sciences
> Texas A&M University
> College Station, Texas 77843-4475
> Telephone: 979-845-3541
> Fax: 979-847-8863
> e-mail: ncohen at cvm.tamu.edu
> 
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-- 
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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