calcBayesCI

A <code>QSarray</code> object, as generated by either makeComparison or aggregateGeneSet

QSarray

the lower and upper bounds of the confidence interval.

low, up

a logical indicating whether the VIF should be used to calculate the variance of the pathway.

addVIF


   A function to calculate the confidence intervals for each of the gene sets in the <var>geneResults</var> object
 

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
(cbolen1@gmail.com) or Steven Kleinstein
(steven.kleinstein@yale.edu)

Christopher Bolen

qusage

qusage: Quantitative Set Analysis for Gene Expression

calcBayesCI function

A function to calculate the confidence intervals for each of the gene sets in the <var>geneResults</var> object

calcBayesCI: Calculate pathway Confidence Intervals

Description

Usage

Arguments

Value

Details