Plot.all: Combined visualization of sequential decomposition and...
In GlobalAncova: Global test for groups of variables via model comparisons

Description Usage Arguments Note Author(s) See Also Examples

Plot that combines Plot.genes and Plot.sequential into one graphic.

1	Plot.all(xx, formula, model.dat = NULL, test.genes = NULL, name.geneset = "")

`xx`	Matrix of gene expression data, where columns correspond to samples and rows to genes. The data should be properly normalized beforehand (and log- or otherwise transformed). Missing values are not allowed. Gene and sample names can be included as the row and column names of `xx`.
`formula`	Model formula for the linear model.
`model.dat`	Data frame that contains all the variable information for each sample.
`test.genes`	Vector of gene names or gene indices specifying a gene set.
`name.geneset`	Name of the plotted geneset.

This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.

Ramona Scheufele ramona.scheufele@charite.de
Reinhard Meister meister@tfh-berlin.de
Manuela Hummel m.hummel@dkfz.de
Urlich Mansmann mansmann@ibe.med.uni-muenchen.de

Plot.genes, Plot.sequential, GlobalAncova.decomp, GlobalAncova

data(vantVeer)
data(phenodata)
data(pathways)

Plot.all(vantVeer, formula = ~ ERstatus + metastases + grade, model.dat = phenodata, test.genes = pathways[[3]], name.geneset = "cell cycle pathway")

Loading required package: corpcor
Loading required package: globaltest
Loading required package: survival
Warning messages:
1: In anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable
2: In anova.lm(lm(dummy.formula, model.dat)) :
  ANOVA F-tests on an essentially perfect fit are unreliable