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This is particularly the case in the setting where one antigen has a strong signal and the other a weak one, the weak signal may not be detected by the permutation resampling method.
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They demonstrated that in some settings their method outperformed the permutation resampling method in terms of sensitivity in detecting responses at the antigen level.
Moodie et al. then compared an ER, the permutation resampling approach and their proposed DFR eq) method, using real and simulated data.
They showed that the permutation resampling approach with the Westfall Young adjustment for multiple comparisons generates the desired false positive rate while remaining competitive with the other methods in terms of overall sensitivity.
Geneset permutation was chosen to achieve enough statistical power for permutation resampling due to the small number of samples.
They also propose two STs based on a bootstrap and permutation resampling approach where the data are pooled across all antigens.
To account for the small number of replications, exact P-values of the KW tests were computed using a permutation resampling method (21) to perform 1.0E6 permutations.
Based on this model and by choice of a multiple-testing procedure, expression noises based on permutation resampling can be considerably minimized.
Empirical permutation resampling (p < 0.001) and theoretic Mann–Whitney U test (p < 10−30) statistics indicate that mRNAs corresponding to complex disease SNPs via eQTL associations are likely to be regulated by a larger number of SNPs than expected.
Significance was tested by the permutation test.
Our findings support the application of statistically-based positive criteria such as the permutation-based resampling approach in assessing HIV vaccine-induced T cell responses.
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