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closeReferee Comments: Referee 2
Posted by PLOS_ONE_Group on 06 Jul 2007 at 14:40 GMT
Reviewer 2's Review
“The technical details seem sound to me. However I have three concerns:
(1) the non-randomness of insertion sites is broadly established, so detailed mathematical methods for verifying it case by case seem unnecessary; otherwise expressed the null hypothesis here seems uninteresting and probably not worthy the mathematical effort in such problems;
(2) the claim that the methods used are superior to simple Monte Carlo p-values and simulations has not been established in this paper, in our opinion; in particular it seems the authors can only obtain an upper bound on the true p-value;
(3) the claim that the mathematical methods are necessary because of problems with computer resources, seems to this reader as overstated. Nonparametric MC p-values are routinely obtained and increasingly are considered the new default method in rapidly expanding genomic questions.
Hence, to accept this paper, this reviewer requests that the authors need to properly qualify their claims of necessity for the mathematics, their claim of superiority over MC p-values, and somehow convince the reader that the null hypothesis (of full randomness) is worthy of such intensive mathematical modeling.”
N.B. These are the general comments made by the reviewer when reviewing this paper in light of which the manuscript was revised. Specific points addressed during revision of the paper are not shown.