I have 2 experimental conditions, each generate a series of values for some genes, like the following:
s1 s2 s3 g1 n11 n12 n13 g2 n21 n22 n23 . . .
s1, s2, s3 are samples; g1, g2, ... are gene names; n11, n12, ... are the corresponding gene expression levels, nij being the expression of gene i in sample j. s1 & s2 belong to one group (treatment), and s3 is the other group (control) by itself.
My biological question: how to find out whether a gene is statistically differentially expressed? Or statistically, what test should I use to find whether ni3 is sinificantly different from ni1 & ni2?