GlobalAncova

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GlobalAncova.

Calculates a global test for differential gene expression between groups


Bioconductor version: 3.7

We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.

Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel

Maintainer: Manuela Hummel <m.hummel at dkfz.de>

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

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GlobalAncova")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("GlobalAncova")
GlobalAncova.pdf PDF R Script
GlobalAncovaDecomp.pdf PDF R Script
Reference Manual PDF

Details

biocViews DifferentialExpression, Microarray, OneChannel, Pathways, Software
Version 3.48.0
In Bioconductor since BioC 1.7 (R-2.2) (18.5 years)
License GPL (>= 2)
Depends methods, corpcor, globaltest
Imports annotate, AnnotationDbi
System Requirements
URL
See More
Suggests Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db, vsn, GSEABase, Rgraphviz
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package GlobalAncova_3.48.0.tar.gz
Windows Binary GlobalAncova_3.48.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GlobalAncova_3.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GlobalAncova
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GlobalAncova
Package Short Url https://bioconductor.org/packages/GlobalAncova/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive