I was wondering if anyone has experience working with the TM4 suite (Spotfinder, Midas and Mev) for analysis of microarray. This is the only microarray software suite that I can afford (it's free!) and I have some specific questions about various steps in the procedure. specifically:
1) I am using a common reference design for my experiment (labeling each sample with Cy3 and co-hybridizing it with a reference sample that is the pool of all individuals labeled with Cy5). I want to know where exactly in the TM4 suite I have to define this experimental design. I kind of think it should be in the Midas, any experience?
2) Working with the common reference design and TM4 suite, where can I incorporate biological replicates?
sorry for a long question, any input is highly appreciated