qusage - qusage: Quantitative Set Analysis for Gene Expression
This package is an implementation the Quantitative Set
Analysis for Gene Expression (QuSAGE) method described in
(Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene
Set Enrichment-type test, which is designed to provide a
faster, more accurate, and easier to understand test for gene
expression studies. qusage accounts for inter-gene correlations
using the Variance Inflation Factor technique proposed by Wu et
al. (Nucleic Acids Res, 2012). In addition, rather than simply
evaluating the deviation from a null hypothesis with a single
number (a P value), qusage quantifies gene set activity with a
complete probability density function (PDF). From this PDF, P
values and confidence intervals can be easily extracted.
Preserving the PDF also allows for post-hoc analysis (e.g.,
pair-wise comparisons of gene set activity) while maintaining
statistical traceability. Finally, while qusage is compatible
with individual gene statistics from existing methods (e.g.,
LIMMA), a Welch-based method is implemented that is shown to
improve specificity. The QuSAGE package also includes a mixed
effects model implementation, as described in (Turner JA et al,
BMC Bioinformatics, 2015), and a meta-analysis framework as
described in (Meng H, et al. PLoS Comput Biol. 2019). For
questions, contact Chris Bolen ([email protected]) or Steven
Kleinstein ([email protected])
