PCA and DE analysis for loop design microarray

Question

[predeus]

Hi all,

I am working on a piece of data of a kind I've never dealt with before, and I'd like your input if anybody has experience dealing with things like this. I have an Agilent two-color microarray with 8 sub-arrays (1_1.. 1_4, 2_1..2_4) that involve 3 conditions (Control, Delta, NS). Biological replicas were combined into one pool each (don't ask), so there's basically only technical variation to assess.

If you can help me with suggestions how can I analyze it I would appreciate it. Here's is the design scheme:

[Sean Davis]

You mention two-color arrays. Is this a common reference design?

[predeus]

This is known as a "loop design". It is flawed (in this particular case) since the replicates were all mixed together, but otherwise it has its pros, from what I've gathered from the literature.