[BioC] Limma, dye-swaps and uneven numbers of replicate arrays

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Thu Jun 1 12:38:02 CEST 2006


A simple question really - I have five biological replicate RNA samples.
Each will have cells untreated vs treated, so that's five arrays.  I
want to do dye-swaps, but that means I can have 2* Cy5/Cy3, and 3*
Cy3/Cy5. Do I need to compensate for this "imbalance"?  How do I do it
in limma?


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