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We based our tests on the mammalian phylogenetic tree by Bininda-Emonds et al. [38] with updated branch lengths [39].
In order to test the performance of the proposed method on four-taxon trees, we based our tests on the tree space proposed by Huelsenbeck [ 17], so that it is possible to compare our results to those obtained there with different phylogenetic reconstruction methods.
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We based our test on simple BLAST results, and it may be argued that this sounds neither attractive nor novel.
We are indeed looking for outliers in a null distribution that takes into account selective constraints acting on pathways and past demographic effects, whereas we previously based our test on a null model of human evolution only taking into account global levels of differentiation between human populations.
For any gene with n (log- expression valog- expressionon 1 and m (log-)expression values in condition 2, we can base our test on where and are the sample variances of the expression values in condition 1 and 2, respectively.
We based our test selection on the literature on cognitive dysfunction in type 2 diabetes, previous studies from our group, and recommendations on the assessment of cognitive dysfunction in the context of vascular disease (2, 17).
We based our association tests on the raw intensities in order to avoid the known loss of information and statistical power resulting from classifying raw copy number measurements into discrete classes, i.e. CNV calls (36, 37).
We based our analysis on original test plans, the U.S. EPA comments, and test plan revisions available from the HPV program (U.S. EPA 2012d) as of January 2010.
Based on our test on 92 CASP9 targets, our predicted absolute local qualities have an average difference of 2.60 Å with the actual distances to native structure.
For phylogenetic tests, we based our analyses on Purvis (1995) composite estimate of primate phylogeny.
21 We based our sample size on testing the null hypothesis of a difference of >0.22 between the two treatments.
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