I am new to micro array analysis. We have done 12 agilent single color expression arrays. Now i have data in .txt format which is generated by array scanner. Of these arrays, we have three time points (d0, d1, d2) and each time point with untreated and treated. Besides this each sample we have in duplicates, in total 12 arrays. I tried to take mean value from these duplicates but unfortunately there is lot of standard deviation. Now I assume that I have to do quantile normalization. Can some one explain me how to do this in excel? Would be great if you can provide me a template file. Thanks in advance for your help.
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