Hello, I have a question regarding fiher-test & differential gene expression. I usually use ttest to see which genes are differential expressed between two sample-types. I thought of using fisher test for the first time, to see if results are comparable, yet I'm not shure if I applyed it correctly. I made a 2x2 contingency table for each gene, like: Notch1-Normal Notch1-Tumor up x x2 down y y2 x = Sum of all foldchanges from normal samples (min foldchange = 1.5) y = Sum of all foldchanges from normal samples (max foldchange = 0.5) ...analogue for tumor samples. Then I applyed Fisher test: tab<-c(x, x2, y, y2) fisher.test(tab, alternative="two.sided") Yet I got no significant results (as compared to the t-test results, which harbor some good hits) - so I assume I did'n built the table the right way. I would be greatfull for an example, especially regarding that contingency table. best regards, Noemi