MAMA (version 2.2.1)

metaMA: Wrapper function for effect size or p-value combination methods

Description

This is a wrapper function for effect size or p-value combination as implemented in metaMA package.

Usage

metaMA(data, varname, moderated = c("limma", "SMVar", "t")[1], BHth = 0.05, which = c("pval", "ES")[1])

Arguments

data

MetaArray object containing gene expression data matrices, clinical data matrices and a vector of data set names. The gene expression data matrices must have equal rownames

varname

Character String - name of one column in clinical data matrices to be used as class labels

moderated

Character - method to calculate the test statistic (or p-value) inside each study, one of: "limma", "SMVar" and "t"

BHth

Numeric - threshold for Benjamini Hochenberg adjusted p-values for selection of significant genes in meta-analysis

which

Character - choose "pval" for combination of p-values, or "ES" for effect sizes

Value

An object of class "metaMA.res". It is a list where:

Study1

Vector of indices of differentially expressed genes in study 1. Similar names are given for the other individual studies.

AllIndStudies

Vector of indices of differentially expressed genes found by at least one of the individual studies.

Meta

Vector of indices of differentially expressed genes in the meta-analysis.

TestStatistic

Vector with test statistics for differential expression in the meta-analysis.

References

Marot, G., Foulley, J.-L., Mayer, C.-D., Jaffrezic, F. Moderated effect size and p-value combinations for microarray meta-analyses.

See Also

pvalcombination, EScombination

Examples

data(ColonData)
pv<-metaMA(ColonData, "MSI", moderated = "t")