[BioC] How would I normally compare swirl?

[michael watson (IAH-C)]

Hi

I have a dataset which is pretty much IDENTICAL to the swirl dataset:

Experiment 1 - two replicate arrays with a dye swap:

TreatedCy5 vs UntreatedCy3
UntreatedCy5 vs TreatedCy3

Experiment 2 - two replicate arrays with a dye swap:

TreatedCy5 vs UntreatedCy3
UntreatedCy5 vs TreatedCy3

This is fantastic because I can basically just copy and paste the
instructions from the limma userguide.pdf document to get my
differentially expressed genes.  

However, I want to do a comparison of limma with a "normal" method of
analysis - say a t-test.  How would I carry out a t-test on this kind of
data?

For example, the top gene limma pulls out has these values for my four
arrays for log2(Cy5/Cy3):

-2.7, 2.7, -2.7, 3

This makes sense as the experiment contains a dye-swap, so if I flip my
log(ratios) such that I am always comparing treated/untreated, my values
are -2.7, -2.7, -2.7 and -3.  BUT how would I go about doing a t-test on
this kind of comparison???  (I know there are huge arguments against
doing such a thing, but humour me).  I mean, I basically have four
values for the same thing (the relative expression of treated against
untreated) and if I was doing a t-test - what am I comparing the values
against?  

Thanks in advance

Mick