Thanks Smith for your quick response. Thanks for pointing out the log2 transformation problem in my code. You are correct, I was following GEO2R code.

I will also like to confirm with you if my design matrix is correct for a two color experiment with common reference where the samples are paired (cancerous and adjacent noncancerous tissues were obtained from same patient).

Thanks & Regards,
Shruti Marwaha

Graduate Student
Systems Biology and Physiology
University of Cincinnati
Medical Science Building,
231 Albert Sabin Way
Cincinnati, OH, USA 45267


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