[BioC] Paired two-color design

[January Weiner]

Dear Gordon,

thank you for your quick answer.

> Are your dye-swaps technical replicates of the same RNA samples?  That is,
> does "A1" refer to same RNA sample for the second array as does for the
> first?

Yes, they are dye-swaps only; the biological replicates are A1, A2, ..

> lmscFit() can't be used in conjunction with technical replicates, including
> dye-swaps.

In that case, I'm totally lost. I have no idea how to bite the second
part of my problem, the search for the interaction between treatment
and group.

> On the other hand, your paired design is exactly of the form discussed on
> page 41 of the limma User's Guide (dated 10 June 2012):

This is true. However, it was an attempt on the way to achieve the
goal in the second part. I have no idea how to do it without
separating the channels. Yes, had I designed the experiment, it would
have been another design, but I can't go back in time.

The two groups (mouse strains, actually) differ in their expression.
However, the strains respond very differently to the treatment, and
the goal is to find how these differences in response are on the gene
expression level. The interaction (treatA-ctrlA)-(treatB-ctrlB) is
what I want to test, but I don't know how to do it with the existing
setup.

Kind regards,

j.

-- 
-------- Dr. January Weiner 3 --------------------------------------