[BioC] Paired Samples & Two-Color arrays in limma

[John Fowler]

Hello all,

I have a question about setting up blocks for paired samples in limma.  In
reading the user guide, limma book chapter, & mailing list, I have noticed most
of the questions about paired samples are with Affy chips.  However, I have a
two-color experiment, so I am not sure how to deal with my design.  I hope to be
able to use the duplicateCorrelation function, as suggested by the list, but am
really stumped about the block vector.

I have two samples (of my three) in pairs from a developmental time course (2
time points).  The third sample is a baseline REF sample that is not paired. 
There are 4 biological reps for each sample type.

My hyb design is below:

----->  Ref  -----
| ----       <--- |
| |             | |
| √             | √
ExpT1 -------> ExpT2
      <------- 

Slide	Cy3   Cy5
-----   ---   ---
1	T1a   T2a
2	T2b   T1b
3	Ref   T1c
4	T1d   Ref
5	T2c   Ref
6	Ref   T2d

Here the a, b, c, and d designate the pairs at each Time point.

So, the problem here is that slides 1 & 2 are each pairs, by themselves.  And,
slide 3 could be paired with slide 5, based on the T1c & T2c - but the Ref
samples they are hybed with are not in pairs.

Would this be set up as something like: c(1, 2, 3, 4, 3, 4) ??


Any suggestions here are greatly appreciated!

John

John Fowler
fowlerj at science.oregonstate.edu
Assoc. Professor, 
Botany & Plant Pathology, 
Oregon State University