GlobalAncova

Package: GlobalAncova
Title: Calculates a global test for differential gene expression
between groups
Version: 3.40.0
Date: 2010-02-16
Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with
contributions from S. Knueppel
Description: 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.
Maintainer: Manuela Hummel <m.hummel@dkfz.de>
Depends: methods, corpcor, globaltest
Imports: annotate, AnnotationDbi
Suggests: Biobase, annotate, GO.db, KEGG.db, golubEsets, hu6800.db,
vsn, GSEABase, Rgraphviz
License: GPL (>= 2)
biocViews: Microarray, OneChannel, DifferentialExpression, Pathways
NeedsCompilation: yes
Packaged: 2016-05-04 02:56:20 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GlobalAncova' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c GlobalAncova.c -o GlobalAncova.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ludcmp.c -o ludcmp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c matrix.c -o matrix.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/GlobalAncova/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'GlobalAncova'
    finding HTML links ... done
    GlobalAncova-methods                    html  
    GlobalAncova                            html  
    GlobalAncova.closed-methods             html  
    GlobalAncova.closed                     html  
    GlobalAncova.decomp                     html  
    Plot.all                                html  
    Plot.genes-methods                      html  
    Plot.genes                              html  
    Plot.sequential                         html  
    Plot.subjects-methods                   html  
    Plot.subjects                           html  
    colon.normal                            html  
    colon.pheno                             html  
    colon.tumour                            html  
    genesettesting                          html  
    pair.compare                            html  
    pathways                                html  
    phenodata                               html  
    vantVeer                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GlobalAncova)
Making 'packages.html' ... done