
Dear all,I have data from affy HT430mgpm and I need to analyze the data for differential expression and pathway analysis. I have 3 wildtype controls (Wt neurospheres 2 and 3) for the control analysis.  I have two other tumors  (1509 and 1701) for the analysis. From the cel files, it doesn’t appear that we did replicates for the tumors, just one each, the rationale at the time being that we had wanted to first quickly scan the tumors for common signatures. Those genes that are clearly highly expressed should however represent additional oncogenic signatures, that may stem from the same or related activating pathways.For now, my analysis for controls should give me an accurate expression data for the controls. The tumors will have to be compared across the samples to look for the low hanging fruits.??I am not sure how do I go about doing this since I have 3 replicates for the control but 1 each for different tumors. What should be the strategy that I should use in order to do my analysis.
Thanks,Himanshu Sharma 		 	   		  
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