Genome biology · 2019 · 64 citations · 25 references
Life SciencesBioinformaticsBiostatisticsGene ExpressionGene Expression AnalysisGenomic Data AnalysisDifferential Expression AnalysisDifferential Gene Expression AnalysisGene Expression ProfilingDifferential Gene ExpressionExpression Fold Change AnalysisFalse Coverage-statement Rate ControlFalse Discovery RateFalse Discovery Rate ControlFold Change AnalysisP-valuesStatistical Analysis Of Differential Expression
Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purpose. As an alternative, we propose a method of ranking by confidence bounds on the log fold change, based on the previously developed TREAT test. These confidence bounds provide guaranteed false discovery rate and false coverage-statement rate control. When applied to a breast cancer dataset, the top-ranked genes by Topconfects emphasize markedly different biological processes compared to the top-ranked genes by p value.
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