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?


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]]

