[BioC] question about design

[J.delasHeras at ed.ac.uk]

I have a number of slides from different experiments and I would like 
to combine them in a model to be able to make contrasts between 
conditions not compared directly, and I am wondering what would be the 
best way to do that.

It started as a simple comparison, and things were added later, so 
that's why the design is not as it would have been if we had sat down 
at the beginning and decided what to do...

I have two normal cell lines, call them N1 and N2.
I have two cancer cell lines, call then C1 and C2.
Then I have a treatment on each cancer line, call them C1T and C2T.

The direct experiments performed were:

N1 vs C1
N1 vs C2

N2 vs C1
N2 vs C2

C1 vs C1T
C2 vs C2T

each containing 3-4 slides.

I'm thinking that the simplest way would be to make two models, one 
with C1 as reference, and another with C2 as reference:

N1 vs C1
N2 vs C1
C1T vs C1 ... and similarly for C2.

Of course, it doesn't compare C1 vs C2, or C1T vs C2T, which may be 
interesting.
I've only analysed very simple designs before, and I'm not quite sure 
what would be the best way to combine all this in a reasonable way.
I can use part of the data to answer all my questions of interest... 
but since everything is related directly or indirectly, I guess there 
must be a way to take advantage of all of the data...

any pointers much appreciated!

Jose

-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK