[BioC] One chip analysis...

James W. MacDonald jmacdon at med.umich.edu
Thu Mar 10 21:42:22 CET 2005

Khan, Sohail wrote:
> Hi All,
> I am new to Microarray Analysis and this list.  I posted this before, I don't know if it was posted correctly.
> I want to analyze just one chip..........Is limma suitable for this?  Could you suggest any other package.
> Thank you very much.

Your previous question was posted correctly. Unfortunately there is no 
package for the analysis of a single chip (especially if you are talking 
about an Affy chip...). With a single cDNA chip, all you can do is 
normalize the cy5 and cy3 values, compute the log ratios, and then look 
for genes that have a value larger (in absolute terms) than some cutoff 
(the traditional cutoff being 2-fold). You could certainly use limma for 
the intra-chip normalization, but at that point I think you are done.

If you are using an Affy chip, you should note that the expression 
measures are *relative* values, and are meaningless without something to 
compare to.



> Sohail Khan
> Scientific Programmer
> Genome Research Center
> 500 Sunnyside Boulevard
> Woodbury, NY 11797
> (516)422-4076
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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