# GlobalAncova v3.40.0

## Calculates a global test for differential gene expression between groups

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.

## Functions in GlobalAncova

Name | Description | |

Plot.subjects | Subjects Plot for GlobalAncova | |

GlobalAncova.closed-methods | Methods for Function GlobalAncova.closed | |

colon.normal | Gene expression data | |

Plot.subjects-methods | Methods for Function Plot.subjects | |

Plot.genes | Genes Plot for Global Ancova | |

vantVeer | Gene expression data | |

GlobalAncova-methods | Methods for Function GlobalAncova | |

Plot.genes-methods | Methods for Function Plot.genes | |

pathways | Cancer related pathways | |

phenodata | Covariate information for the van t'Veer data | |

GlobalAncova.decomp | GlobalAncova with sequential and type III sum of squares decomposition and adjustment for global covariates | |

GlobalAncova gene set testing methods | Gene set testing of gene set databases using GlobalAncova | |

GlobalAncova | Global test for differential gene expression | |

GlobalAncova.closed | Closed testing procedure for testing several groups of genes using GlobalAncova | |

colon.tumour | Gene expression data | |

Plot.all | Combined visualization of sequential decomposition and influence of single genes on the GlobalAncova statistic | |

colon.pheno | Covariate information for the colon data | |

pair.compare | Pairwise comparisons of factor levels within GlobalAncova | |

Plot.sequential | Visualization of sequential decomposition | |

No Results! |

## Last year downloads

## Details

Date | 2010-02-16 |

License | GPL (>= 2) |

biocViews | Microarray, OneChannel, DifferentialExpression, Pathways |

imports | annotate , AnnotationDbi |

suggests | Biobase , GO , GO.db , golubEsets , GSEABase , hu6800 , hu6800.db , KEGG , KEGG.db , Rgraphviz , vsn |

depends | corpcor , globaltest , methods |

Contributors | M. Hummel, U. Mansmann, R. Meister, R. Scheufele |

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