To install this package, start R and enter:

## try http:// if https:// URLs are not supported

In most cases, you don't need to download the package archive at all.



qusage: Quantitative Set Analysis for Gene Expression

Bioconductor version: Release (3.2)

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. For questions, contact Chris Bolen ( or Steven Kleinstein (

Author: Christopher Bolen and Gur Yaari, with contributions from Juilee Thakar, Hailong Meng, Jacob Turner, Derek Blankenship, and Steven Kleinstein

Maintainer: Christopher Bolen <cbolen1 at>

Citation (from within R, enter citation("qusage")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


To view documentation for the version of this package installed in your system, start R and enter:



PDF Running qusage
PDF   Reference Manual


biocViews GeneSetEnrichment, Microarray, RNASeq, Software
Version 2.2.0
In Bioconductor since BioC 2.13 (R-3.0) (2 years)
License GPL (>= 2)
Depends R (>= 2.10), limma(>= 3.14), methods
Imports utils, Biobase, nlme, lsmeans
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source qusage_2.2.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) qusage_2.2.0.tgz
Mac OS X 10.9 (Mavericks) qusage_2.2.0.tgz
Subversion source (username/password: readonly)
Git source
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center