I am confused about when I can and/or cannot run an ANOVA on percentage data. MY situation is as follows:
I have two separate treatment groups (T1 and T2). Each of these treatment groups receives 1 of 3 drugs (D0, D3, D30) only once. My DV is muscle activity (continuous data). Only one muscle response is recorded. 3 consistent pre-drug baseline measurements and 3 consistent post-drug measurements are taken.
I take the mean of the pre and post to give single values, and then calculate the post-drug as a % of pre drug for each subject, and then compare mean % for each treatment/drug group
The raw data are generally not normally distributed (though one group out of six comes out as normal but only just)
The problem I have is that pre-drug values are quite variable and so I think it's better to look at the proportion change (if indeed that it the correct thing to do?). Previously I have just expressed the post-drug values as a percentage of the pre-drug (not percentage difference), and then compared the mean percentages of the various different groups with a two-way ANOVA. (nb. the percentage data are normally distributed according to shapiro-wilks test)
So for example, pre-drug value = 500, post drug = 100, thus the % baseline is 0.2 (20%).
Is this a valid comparison?? I am less interested in absolute size of pre or post-drug values. It seems quite logical to me but my stats knowledge is pretty basic.