[BioC] 2 Test Samples on 1 Array

[Sean Davis]

elliot harrison wrote:
> Hi All,
> 
> Not strictly Bioconductor question I'm afraid. Is there any reason why
> we couldn't hybridise 2 samples to one array (1 green, 1 Red) and then
> perform single colour analysis on both samples independently? It would
> be a custom agilent array using the probe set from their whole human
> genome array.

People do this, yes.  I do not know how much crosstalk between channels
there is on modern arrays.  You will want to think a little about
normalization, also.  See the limma user guide for some examples of
one-channel analysis of two-color data.

Sean