Hello, I am new to microarray analysis and would like some feedback on this question: I have clinical samples for four time points for which I conducted miRNA microarray and am using basic expression console and TAC softwares from Affy for analysis. I have only a two samples for my fourth time point and I think it will skew my analysis and am skeptical at incorporating it. My PI still wants to see how the results look including the low sample time point. Should I analyze all four time point samples and generate one analysis or should I analyze first three time points (0, 1, 2 months) and then do a second analysis with all four time points (0, 1, 2, 7 months) and deduce information by comparing these two analyses? Is this even correct to combine two analyses like this?

Please help with this! Thanks VK