Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.
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ABSTRACT:
SUBMITTER: Harrison PF
PROVIDER: S-EPMC6437914 | biostudies-literature | 2019 Mar
REPOSITORIES: biostudies-literature
Publications
Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list.
Harrison Paul F PF Pattison Andrew D AD Powell David R DR Beilharz Traude H TH
Genome biology 20190328 1
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 dat ...[more]
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