[BioC] biological reps and dye-swaps and duplicate spots in a common reference design

Jenny Drnevich drnevich at illinois.edu
Wed Nov 12 18:32:50 CET 2008

Sorry for the re-posting, but the text attributes didn't go 
through... I wanted to make sure to distinguish between Gordon's 
excellent advice and my (hopefully good) advice!

Hi Sylvie,

Here is some advice I got from Gordon Smyth about 2.5 years ago:

 > My approach to designs like this, at
 > least as a start, is to try duplicateCorrelation() on each of the
 > levels separately to get an idea of the strength of the correlation
 > at each level. Very often, some of the levels are so weak that they
 > can be ignored.

So, first ignore the dye-swaps and set up your design matrix as if
you have 10 biological replicates of each strain, then use
duplicateCorrelation() on the duplicate spots. Second, ignore the
duplicate spots, use the same design matrix but use
duplicateCorrelation() with the dye-swap pairs as the blocking
variable.  If the correlation on the dye-swap pairs is not
substantially negative (at least -0.2??), then you could just ignore it and
use duplicateCorrelation() on the duplicate spots. On the other hand,
if the correlation of the duplicate spots is extremely high, you
could just average the values and then use duplicateCorrelation() on
the dye-swaps. This latter option is my preference; see ?avedups for
an easy way to average the duplicate spots.


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