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MiDAS and Rank Product methods efficiently detect true ASEs but they suffer from the lack of multiple test error correction.
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Both gene- and pathway-based analysis deal with the challenge of multiple testing error control (i.e. multiplicity correction ).
Statistical analysis of the data was performed by GeneSpring software (Agilent, Palo Alto, CA) using two-tailed t-tests with the FDR multiple testing error correction set at the p cut-off value of 0.05.
Where there were significant results in tests split by year and method, we checked them further with a Bonferroni simultaneous inference adjustment to control for multiple testing error.
The well-known Bonferroni correction and Benjamini Hochbergg false discovery rate (FDR) test is also included to reduce the effect of multiple testing error.
A staged analytic design applying a priori criteria to the results of conditional logistic regressions was employed to exclude associations likely due to multiple testing error.
Multiple testing error (false-positive results) was estimated by the false discovery rate (FDR = expected/observed) (71) procedure, and median FDRs are reported.
The one-way ANOVA test was used to identify proteins differentially expressed over time in experiments PM1 and WCL1, and was corrected using the method of Benjamini-Hochberg to control for multiple testing error (Benjamini and Hochberg, 1995 ).
Notably, the differences in gene expression found after sham surgery or between control samples did not overlap with the genes found to be responsive to PHx, suggesting that these represent random differences reflecting multiple testing error or biological variability.
Apart from reporting unprotected sex (42.9 %), health risk behavior was not frequently reported.> -wrap-foot> analysesyses have been adjusted for age, methadone dose, and duration of treatment using multivariable regression and for multiple testing error using false discovery rate; results for binary variables reported as OR and results for continuous variables reported as MD.
SAM is a statistically rigorous test that incorporates a FDR calculation to correct for multiple testing errors.
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