[BioC] how to handle pooled replicate?

[Sean Davis]

On 7/31/06 2:49 PM, "Jianping Jin" <jjin at email.unc.edu> wrote:

> 
> Dear list:
> 
> There is a data set, consisting of 3 Agilent slides. The experiment was run
> with direct hybridization, knock-out versus wild-type, and no dye swap. Due
> to difficulty of collecting samples, the samples were pooled and hybridized
> onto 3 separate slides.

How were the samples pooled?  Were they pooled and then split, or are there
three distinct biologic replicates?

The lack of dye swap IS a problem, as you will likely find dye-biased probes
(potentially MANY).

> Of course the 3 slides are not biological replicates. They are not pure
> technical replicates either. How should I set up a design matrix for limma
> model analysis?

You'll need to be a bit more specific about how you did the pooling....

Sean