I think I am reading you correctly. You have two treatment and one control datasets. You have somehow 'normalized' the two treatment groups by the control group and are left with the two 'normalized' treatment datasets. You now want to perform a statistical test to determine if there is a difference in the outcome between the two 'normalized' treatment groups.

If this is the case, and you feel that the data do not meet the assumptions of parametric tests for this kind of data (like the t-test, which assumes the data within each group are normally distributed), then you may use a variety of non-parametric tests. One popular non-parametric test for this kind of data is the Wilcoxon rank sum test. This test is used to test for a difference in the median response between groups.

In R, you can implement the Wilcoxon rank sum test with the command:

wilcox.test()

I suggest that you read the help file before using the test. This can be done with the following command:

?wilcox.test

or

help(wilcox.test)

-Matt