Hi Sean, Members, I am analyzing the microarray data from exposed vs unexposed to metals. The data is single color Agilent platform. I normalized all the arrays and exported as a text file all the green intensities. Now I need to find which are the differentially expressed genes from this single file. How to proceed please help? File Headers for normalized data: ProbeName Genesymbol GeneName Exposed1 Exposed2......Unexposed1 Unexposed2... It would be helpful if you let me know the exact commands as I am a newbie. Regards, Srikanth -- Srinivas M. Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+919019114878 [[alternative HTML version deleted]]

Hi Srikanth, Take a look at the limma User's Guide. There are multiple worked examples. Best, Jim On 9/14/2011 6:02 AM, Srinivas M. Srikanth wrote: > Hi Sean, Members, > > I am analyzing the microarray data from exposed vs unexposed to metals. The > data is single color Agilent platform. I normalized all the arrays and > exported as a text file all the green intensities. Now I need to find which > are the differentially expressed genes from this single file. How to proceed > please help? > > File Headers for normalized data: > ProbeName Genesymbol GeneName Exposed1 Exposed2......Unexposed1 > Unexposed2... > > It would be helpful if you let me know the exact commands as I am a newbie. > > Regards, > Srikanth > > > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues