vantVeer


Normalized gene expression data for the van t'Veer example:
A subset of 96 samples without BRCA1 or BRCA2 mutations and 1113 genes associated with nine
cancer related pathways (see also <code>?pathways</code>) was chosen.


datasets

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.

Manuela Hummel

GlobalAncova

Calculates a global test for differential gene expression
between groups

vantVeer function

The format is: 
<code>num [1:1113, 1:96] 0.13 0.936 -0.087 0.118 0.168 -0.081 0.023 -0.086 -0.154 0.025 ...</code> 
 <code>- attr(*, "dimnames")=List of 2</code>                                      
  <code>..$ : chr [1:1113] "AW025529" "NM_001648" "NM_001753" "NM_003298" ...</code>  
  <code>..$ : chr [1:96] "1" "2" "3" "4" ...</code>

Format

Normalized gene expression data for the van t'Veer example:
A subset of 96 samples without BRCA1 or BRCA2 mutations and 1113 genes associated with nine
cancer related pathways (see also <code>?pathways</code>) was chosen.

vantVeer: Gene expression data

Description

Usage

Arguments

Format

Examples