I am very new to microarray experiments and have a question with calculating
duplicate correlations for 4x44 Agilent chips.

After searching extensively through the bioconductor mailing list
submissions, I have seen that no one has come up with a solution to handling
a variable number of gene replicates on the same chip.  As I understand it,
limma was not designed to handle this.

Before seeing that this was not a functionality of limma, we attempted to
treat each individual gene as a block.  We sorted by probe name, then
assigned a unique number to each probe name with it repeating the number of
times that gene appears on the chip.  We ended up with roughly 21,000
blocks.  I had assumed that duplicate correlation would compute a
correlation for each of these blocks.

Is this a reasonable approach or a complete misunderstanding of the blocking
variable? (By the way, the calculation is still running after an hour)

-- 
Scott Franklin, Ph.D.
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Post-Doctoral Research Associate
Plant and Soil Science
Texas Tech University
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http://blog.drscottfranklin.net

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