Hello, I have p values from two distributions, Pold and Pnew > head(m) CHR POS MARKER Pnew Pold 1: 1 785989 rs2980300 0.1419 0.9521 2: 1 1130727 rs10907175 0.1022 0.4750 3: 1 1156131 rs2887286 0.3698 0.5289 4: 1 1158631 rs6603781 0.1929 0.2554 5: 1 1211292 rs6685064 0.6054 0.2954 6: 1 1478153 rs3766180 0.6511 0.5542 ...
In order to compare those two distributions (QQ plots shown in attach)
does it make sense to use:
var.test(m$Pold, m$Pnew, alternative = "two.sided")
F test to compare two variances
data: m$Pold and m$Pnew
F = 0.99937, num df = 1454159, denom df = 1454159, p-value = 0.7057
alternative hypothesis: true ratio of variances is not equal to 1
95 percent confidence interval:
0.9970808 1.0016750
sample estimates:
ratio of variances
0.9993739
Or some other test makes more sense?
Thanks
Ana
qq-plots-compressed.pdf
Description: Adobe PDF document
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