I have pairs of values from two runs (replicate) for each sample along with total count for each run. I assumed each value as random binomial. I used log-likelihood ratio test to compare each pair, but my data range is wide, e.g. X1, X2 = (0,0), (0,1), (0,2), ..., (20, 20) with total counts for each run (n1, n2) range from hundreds to thousands. So my data look like:
ID X1 X2 n1 n2 A1 0 0 119 230 A2 0 1 213 185 . . . . . . . . . . . . . . . A200 15 23 2300 1735
What test will be appropriate and power for it? Already tried likelihood ratio test, how can I implement Fisher's exact test in R for it? any other test that may use X1 condition of X1 + X2!
Any help will be appreciated. I want to implement it in R, so R codes/function will be more helpful. Thanks in advance