Dream: powerful differential expression analysis for repeated measures designs.
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ABSTRACT: Summary
Large-scale transcriptome studies with multiple samples per individual are widely used to study disease biology. Yet, current methods for differential expression are inadequate for cross-individual testing for these repeated measures designs. Most problematic, we observe across multiple datasets that current methods can give reproducible false-positive findings that are driven by genetic regulation of gene expression, yet are unrelated to the trait of interest. Here, we introduce a statistical software package, dream, that increases power, controls the false positive rate, enables multiple types of hypothesis tests, and integrates with standard workflows. In 12 analyses in 6 independent datasets, dream yields biological insight not found with existing software while addressing the issue of reproducible false-positive findings.Availability and implementation
Dream is available within the variancePartition Bioconductor package at http://bioconductor.org/packages/variancePartition.Contact
gabriel.hoffman@mssm.edu.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Hoffman GE
PROVIDER: S-EPMC8055218 | biostudies-literature |
REPOSITORIES: biostudies-literature
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