I'm trying to compare two groups of ranked lists (of genes) by test of proportion. As shown in the mosaic plot and the data, there is a gene of interest which divides each list into genes ranked above it and below it. I wish to see if there is significant difference in ranking of our gene of interest among the groups (S,N,L and K) which are comprised of two replicates, S1&S2, N1&N2 etc.
Sample Above Below S2 34 809 S1 141 856 N2 62 715 N1 28 864 L2 30 543 L1 33 605 K2 1 542 K1 1 618
For comparison of two single lists I can do a Chi-square test as follows,and get the p-value:
L2_L1.mat <- matrix(c(30,543,33,605),nrow=2,byrow=2) chisq.test(L2_L1.mat,correct=FALSE) Pearson's Chi-squared test data: L2_L1.mat X-squared = 0.0024441, df = 1, p-value = 0.9606 N2_L1.mat <- matrix(c(62,715,33,605),nrow=2,byrow=2) chisq.test(N2_L1.mat,correct=FALSE) Pearson's Chi-squared test data: N2_L1.mat X-squared = 4.4074, df = 1, p-value = 0.03578
But How to compare two groups like L(L1,L2) and N(N1,N2)