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With a binary or time-to-event outcome and a small sample size, we recommend the use of a stratified analysis using random effects, as this has been shown to maintain nominal type I error rates while giving high power.
This demonstrates that, in principle, when randomisation has been balanced within strata, a stratified analysis may be necessary to maintain nominal type I error rates when there are large interactions between balancing factors.
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For case/mother duos, no method maintained nominal type 1 error (Fig. 9).
For case/parent trios, only method 2b maintained nominal type 1 error in the presence of population stratification (Fig. 8).
To try and maintain nominal growth, some officials worry, would allow the bubble to inflate even further.
But Republicans would maintain nominal control of the Senate because Dick Cheney, as a Republican vice president, would cast any vote needed to break a tie.
Results of an extensive Monte Carlo simulation study illustrate that the new approaches effectively maintain the nominal Type I error even for small numbers of clusters.
For the methods that can maintain the nominal type I error rate, statistical power is compared.
IUTA was robust to the read coverage, but both IUTA and Cuffdiff2 failed to maintain the nominal Type I error rate.
A distressing feature of both IUTA and Cuffdiff2 was their failure to maintain the nominal Type I error rate – both rejected the null hypothesis too often when it was true.
Although we found that a permutation approach for the tests IUTA_SKK and IUTA_CQ helped to maintain the nominal Type I error rate (see details in the Additional file 1), the minimum possible p values for permutation tests with few samples can be too large to reach statistical significance after FDR or other genome-wide multiple-comparison adjustment.
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CEO of Professional Science Editing for Scientists @ prosciediting.com