I'm new to "Significance Analysis of Microarrays (SAM) - so could use some input
I have two classes (CON and DM) with 8 subjects in each. Each 'experimental unit' has been measured at 3 different time points (T1, T2, and T3). Thus, I have set the response type/format to "Time course, two class (unpaired)". However, when I run the SAM analysis (in Excel) I only get one list of differentially expressed miRNAs. Do anyone know how I can pin-point miRNA differences at each of the three time points? That is, CON(T1) vs DM(T1), CON(T2) vs DM(T2), and CON(T3) vs DM(T3).
NB. For this particular test in SAM I'm not able to state that my expression values are log2(ratios). Thus, in the result tab named "SAM Output" log scale data is marked as FALSE.