Hello all, For calculating the significance of the overlap of 2 gene lists I use either the Fisher exact test or the hypergeometric distribution. When I tried this on the overlap of 3 gene lists I have to make a 2x2x2 contingency table of what is IN or NOT in a list. Unfortunately the Fisher test cannot handle multidimensional contingency tables. Can someone with statistics background check if the Mantel-Haenszel test can be used to calculate the significance of the overlap of 3 gene lists? My sample code is below. # Here is a case that has an overlap close to that expected by chance. The experiment has 2000 genes, and 3 lists of 50, 100 and 200 genes each. In the overlap of all 3 lists, 5 genes are found. > c.table <- c(5,15, 5,175, 0,80, 40,1680) > dim(c.table) <- c(2,2,2) > dimnames(c.table) <- list(List1=c("in1","not1"), List2=c("in2","not2"), List3=c("in3","not3")) > c.table , , List3 = in3 List2 List1 in2 not2 in1 5 5 not1 15 175 , , List3 = not3 List2 List1 in2 not2 in1 0 40 not1 80 1680 > sum(c.table) [1] 2000 > fisher.test(c.table) Error in fisher.test(c.table) : if 'x' is not a matrix, 'y' must be given > mantelhaen.test(c.table) Mantel-Haenszel chi-squared test with continuity correction data: c.table Mantel-Haenszel X-squared = 1.1764, df = 1, p-value = 0.2781 alternative hypothesis: true common odds ratio is not equal to 1 95 percent confidence interval: 0.764363 5.403287 sample estimates: common odds ratio 2.032258 The test tells me that the overlap is probably due to chance alone, which is what I expected. >From what I understand, the Mantel-Haenszel tells me that it is testing that the overlap of List 1 and List 2 is independent from List 3. To me, that seems like extending the Fisher test to a third dimension (gene list). Thanks for your insights, Edwin -- Dr. Edwin Groot, postdoctoral associate AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032948