[BioC] Use of individual channel from a 2-color array as a measure of expression level?

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 8 19:14:57 CEST 2011

Hi Hari,

On 6/8/2011 12:42 PM, Hari Easwaran wrote:
> Dear BioC gurus,
> Two-color arrays are generally used to compare expression of a test sample
> (like drug treated) relative to control. Usually Cy5 channel is used for the
> test and Cy3 is used for the control. The output from such data that is used
> for any analysis is the log ratios that gives an idea of relative expression
> of genes in the test vs control samples.
> Can the intensities from an individual channel (Cy3) in a two-color
> microarray expression data (in my case Agilent) be used to get a measure of:
> (a) absolute (approximate) expression level (say E) of a gene/probe
> (b) can the Es for a gene/probe from two or more control samples be compared
> to get an idea of the general expression of that gene in the samples. If
> yes, what is the best way to normalize between the Cy3 channels from
> different arrays?

See the limma User's Guide, specifically the section on single color 



> I guess my question is can the individual channels from a two-color array be
> used like a one-color array.
> Sorry if such an issue has been addressed before, but I couldn't get
> anything on the web (the keywords to search on such a topic is damn vague).
> I would appreciate any help/suggestions.
> Sincerely,
> Hari
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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