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("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 | R Script | |
| GlobalAncovaDecomp.pdf | R Script | |
| Reference Manual |
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 |