In reply to Bo Martin.

I don't know the details of your data, but I think you need to look at the design of your experiment and how the data were collected.
Suppose you have 10 males and 10 females in the data set. There are two ways that this can occur:

1. You sampled 20 people. It just happened by chance that 10 were males. If you repeat the experiment, you might end up with 12 males, or maybe 9. In this case, I think you want to resample the whole data set, ignoring strata.
2. You went out and collected data on 10 males. You then went out and collected data on 10 females. If you repeat the experiment, you will always have 10 males and 10 females. In this case, you
would want to resample within each strata.

After you obtain the bootstrap samples, do exactly the same analysis on each sample that you did on the original data.