[R] comparing variances/distributions

[Ana Marija]

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

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