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As discussed in Section "Anomalous signal detection", f i ∗ is anomalous under ℋ 1 i, and our goal is to control the FDR below a user-specified false discovery level δ.
While we selected 1.5 SD's from the mean of the opposite group, this number can be changed depending on the false discovery level acceptable to the experimenter.
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Significant pathways are identified at false discovery rate level 0.05.
The false discovery rate level was set at 5% [ 22, 23].
Considering a false discovery rate level of 5% seems inappropriate since it leads to select too many genomic areas (>80%).
We used R[ 50] to calculate p-values with Fisher's Exact Test and employed the package 'qvalue'[ 51] to correct for multiple testing setting a false discovery rate level at 0.001.
Approximately half of all genes return no results, while a handful return hundreds of results at extremely small false discovery rate levels, reflecting high linkage disequilibrium (but note that the database does not yet include imputed SNPs).
We define genome-wide significance using the definition of family-wise error; our goal is to control the probability of making one or more false discoveries at level α.
The robust method was used and False Discovery Rate (FDR) level was set at 0.05.
The FUNC hypergeometric test was performed with 5000 random sets [31], which identified many GO groups that are significant at a false discovery rate (FDR) level of 5%.
For control of the false discovery rate at level α search i ∗ = max { i : p r i ≤ i m α }.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com