Iran Malavazi - 2011-09-28

Dear all
We have been using TMEV for a while, but now I want to change the way of analysis. We used to perform one class t-test. Now I want to use SAM, for example. The problem is I don’t know how to enter data in this case.

We have for example the following experimental which is a recurrent design in our lab (two color Agilent slides and protocol, with 4 replicates each point):

Wild type strain grown for 1 hour       x          mutant strain grown for 1 hour
Cy3                                                                                     Cy5 

Wild type strain grown for 1 hour       x          mutant strain grown for 2 hour
Cy3                                                                                     Cy5 

Wild type strain grown for 1 hour      x          mutant strain grown for 4 hour
Cy3                                                                                  Cy5 

So, there are 12 hybridizations. Let’s suppose I want to use SAM analysis module in MEV. In this kind of experiment, can I consider it a two class unpaired? If so, how I should arrange the data in groups in the test window? How can I arrange the data in two groups for analysis if I use two-color labeling?

I hope someone can help me.
Thank you very much