Hi Edmund, > I started using the toptables for differentially expressed genes. I am > confused about "B statistic"? I gather that the larger the B > statistic, the more significant the gene expression. But what sort of > statistical test is it? Please change the subject line to include "B statistic", if that is the focus of your question. The B statistic is the log odds of differential expression (also known as a lod score). Bascially if it is greater than 0 then you have more than a 50/50 chance that your gene is truly differentially expressed given its fitted M value (listed in the top-table) The original B statistic is described in Lonnstedt and Speed's "Replicated Microarray Data" : http://stat- www.berkeley.edu/users/terry/zarray/TechReport/Baypap4d.pdf (In particular, see Appendix A.1) It has been modified slightly by Gordon Smyth in the limma package. Regards, James