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Common reference design and TM4 suite

Common reference design and TM4 suite - Microarrays Forum

Common reference design and TM4 suite - Microarray Forum. Discuss array technology and Gene Chips. DNA microarray and Protein arrayit forums.


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Old 01-27-2010, 06:00 PM
Pipette Filler
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Default Common reference design and TM4 suite



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
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