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To single out significant tests in a group, raw significance probabilities were corrected by the sequential Bonferroni method for multiple independent tests as indicated in [60].
In the study we have presented raw significance levels as well as the Bonferroni values corrected for multiple testing.
The moderated t-statistics was applied and was used for assessing the raw significance of differentially expressed genes.
The moderated t statistics was applied in a pairwise fashion (each treatment was compared to its own control) and was used for assessing the raw significance of differentially expressed genes.
The FDR threshold q, illustrated as the horizontal dashed line in Figure 3D, is a data-determined quantity (Benjamini and Hochberg, 1995 ) that is substantially less than the raw significance level of 0.05 (in this case, q < 0.01).
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The TSP effects on TLC remained unchanged, whereas the short-term TSP effect on Raw lost significance when additionally adjusting for SO2.
PERMANOVA+ was run using Type I sums of squares, unrestricted permutation of raw data, and significance was determined by permutation test (10,000 permutations) of the pseudo-F statistic.
The raw threshold of significance was p = 0.05.
No transformation of the two raw variables reached significance.
Raw data and significance for all paralytic editing sites in engineered mutants.
The list of significantly changed probe sets shown in Figure 1 was obtained after filtering by signal intensities (20 100th percentile in the raw data), statistical significance (P<0.05, unpaired t-test) and fold change (>2.0) using GeneSpring GX software (Agilent Technologies, Santa Clara, CA).
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