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Exact(19)
Employing strict significance thresholds when testing individual SNPs avoids false positives at the expense of increasing false negatives.
We explore, in a two-stage design, how the use of false discovery rate (FDR) can alleviate the burden of a prohibitively strict significance level for single marker tests and still control the number of false positive findings, when there is more than one causal variant.
We therefore conducted simple, robust statistical analyses with strict significance thresholds.
We use this strict significance level because of the number tests and the sensitivity of the analysis.
Although rare, we noted several genes that may be changing to a larger degree, but which fell below a strict significance threshold, for example ZIC3 in brain.
The higher number of patients in the main study yielded a higher statistical significance, revealing over-representation of PANTHER categories such as Extracellular matrix structural protein, which in the pilot study did not meet the strict significance criterion (p-value<0.01 with Bonferroni correction).
Similar(41)
We chose a significance level of p ≤ 0.05, but if a stricter significance level p ≤ 0.01 is chosen there were still significant differences between high/low SOC subgroups in outcome.
The disparity filter requires a very high significance level (i.e., large probability) to recover the expected geometry, and with stricter significance criteria the network is completely disconnected (i.e., no meaningful underlying geometry is discovered).
This effect is lessened if one uses a stricter significance level.
Considering a risk of mass significance the results at a stricter significance level of p ≤ 0.01 is pointed out.
Smaller, i.e. stricter, significance levels well below 10-10, on the other hand, do not change the coefficients of variation, either (data not shown).
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