Common reference design and TM4 suite - (Jan/12/2010 )

Greetings everyone,

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

Kaveh

I'm a bench guy, so I am not good at data analysis...we use Agilent Genespring...its available for a full option one month trial period ...you can also get pdf helpfiles with everything that u need to know to do data analysis !

http://www.chem.agilent.com/en-US/products...es/default.aspx