[BioC] LIMMA: Technical replication (dye swap) and within-array replicate spots

[Pie Muller]

Sorry, didn't see that this question has been addressed earlier... Still 
what would you suggest? Compute the mean values from the replicate spots on 
each array after normalisation and use those for fitting the linear model, 
or neglecting the "block" effect of the dye-swap? A similar problem occurs 
if one considers separate channel analysis of two-colour data.

What is the best way to create a new MAlist object with means from my 
original object containing the values for each replicate spot? To use the 
function "aggregate"? Couldn't figure out with my basic R knowledge...

Thanks,
Pie



Dear Gordon,

I am analysing a simple two-colour microarray experiment camparing strain A 
vs. strain B with 3 biological and two technical replicates (dye swap). 
Hence, my experiment is similar to your example in section 11.1 of the 
limma user's guide. Our array has four within-array replicate spots for 
each gene. As the "block" argument in the limma function "lmFit" must be 
NULL if ndups is larger than 2 I wonder how I can handle both technical and 
within-array replicates?

In advance, many thanks for any suggestions!

Pie




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Dr Pie Mueller

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