Performing a two-sample t-test comparing the means of the two treatment groups at each of the 12 weeks (provided the data are Normally distributed in each group in each week and the variances in the two groups are equal at these times).
Taking the baseline reading (ie the reading at week one) from the subsequent readings for each patient, and comparing the changes from baseline in the two groups at each of weeks 2 to 12 by performing a two-sample test (such as the t-test or a non-parametric test such as the Wilcoxon rank sum test) at each of these weeks.
Taking the average of the readings for a patient and using these averages instead of the raw readings in the analysis. The comparison of the two treatment groups is achieved by comparing the averages in the two groups by a two-sample test (such as the t-test or a non-parametric test such as the Wilcoxon rank sum test).
Performing a two-sample test (such as the t-test or a non-parametric test such as the Wilcoxon rank sum test) comparing all the readings in one treatment group with those in the other treatment group.
Finding the area under the curve for each patient and comparing these areas in the two groups by performing a two-sample test (such as the t-test or a non-parametric test such as the Wilcoxon rank sum test).