Hi,

On page 36-37, the user's guide of LIMMA (18 April 2007) gives example and
explains about Technical Replication as follows :


FileName Cy3 Cy5

File1       wt1 mu1

File2       wt1 mu1

File3       wt2 mu2

File4       wt2 mu2



The first and second and third and fourth arrays are technical replicates.
It would not be correct to treat this experiment as comprising four
replicate arrays because the technical replicate pairs are not independent,
in fact they are likely to be positively correlated. One way to analyze
these data is the following:



> biolrep <- c(1, 1, 2, 2)



[Below it also gives one more example: -]



.... If the technical replicates were in dye-swap pairs as



FileName Cy3 Cy5

File1        wt1 mu1

File2        mu1 wt1

File3        wt2 mu2

File4        mu2 wt2



then one might use

> design <- c(1, -1, 1, -1)



Now, I'm wondering how (1, 1, 2, 2) or (1, -1, 1, -1) has been picked
respectively from those two tables !



It looks to me that in the first case the 1's and 2's are saying that the
pairs of arrays are replicates, so they get the same number.

In the 2nd table, [File 1 & File 2] are inverses but are linked (because of
Wildtype 1 & Mutanttype 1). Accordingly, [File 3 & File 4] - are also
inverses & linked to themselves (because of the presence of wildtype 2 &
mutant 2). If that is the case, I am wondering that it should have been more
logical to use something like (1, -1, 2, -2) instead of the given (1, -1, 1,
-1) !!



Or, is there anything else which is being considered here (and I don't know
yet)

Chintanu

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