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reviewer comments

Posted by sezgine on 10 Apr 2008 at 15:53 GMT

what were some the pozitive and negative comments you got from earlier submission of this work? What did you improve, what you couldnt address and why?

RE: reviewer comments

oleksyk replied to sezgine on 16 Apr 2008 at 23:51 GMT

A good thing about PLoS ONE is that they posted all my reviewers comments (See Reviewers comments 1 and 2 threads), so I could post my answers to all the questions asked by the reviewers, and especially those that did not quite make it to the paper. You can look through those if you like, but I would only mention one thing they asked me and I didn't do.
1). Since most of the selection papers are concentrated on the HapMap as a resource, reviewers constantly asked me to run my program on HapMap. While I did that, I didn't want to take the attention from the fact that this approach can be applied to a much smaller dataset. In the end I even had to change the title to emphasize the "light coverage dataset".
2). The other point that have never changed, and insisted upon is using variance in the moving window scans for Fst. Because of the alternating fixation of alleles on selected haplotypes, the mean value may not be as good, but the variance captures this phenomenon nicely.