[BioC] Dealing with technical replication with a common reference design

[michael watson (IAH-C)]

Hi

I have to say the limma userguide is now one of the most comprehensive
guides available for microarray analysis.  It is therefore regretfully
that I ask for additional information...

The guide rightly points out that we must not treat arrays that are
technical replicates as true replicate arrays as they are not
independent.  Sections 10.1 and 10.2 then go on to explain how technical
replicates can be handled using either duplicateCorrelation or by
manipulating the contrasts matrix.  However, both these examples deal
with arrays where direct comparisons have been made.  

I have data from a common reference design, comparing two groups using a
common reference, with biological replicates and technical replicates
(dye swaps) and it's not immediately clear from the examples how I
should deal with the technical replication.

Many thanks for any hints forthcoming!

Mick