[BioC] how to handle pooled replicate?
sdavis2 at mail.nih.gov
Mon Jul 31 20:55:11 CEST 2006
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
> 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....
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