Hi all,

I am using the limma package to analyze a multi-species cDNA array, 2-colour
reference design.  The problem is that because it is a multi-species (and
tissue) array, and I am querying only 1 tissue, only 1/3 of the 15,000 spots
appear to correspond to cDNA in my samples, and the number of spots that
actually get tested is around 3,500.  These spots are rather randomly
located across the slides because of many libraries used in construction of
the array.

Before I get too far into my analysis, I read in the limma guide that
print-tip loess within-slide normalization is not always a good choice for
data with 'small' print tip groups.  I am assuming that a global loess
normalization is the more appropriate approach in my case.

Is my assumption reasonable?

With thanks

Adrian M.


PS - I'm running R 2.3.1, limma 2.7.3, and limma GUI version 1.8.1

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