ssStatistic: Calculate single study estimates of effect size

In XDE: XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Description

Calculate single study estimates of effect size for lists of ExpressionSets

Usage

ssStatistic(statistic = c("t", "sam", "z")[1], phenotypeLabel, esetList, ...)

Arguments

statistic	Character string indicating Welch t-statistic (t), SAM (sam), or a z-statistic (z)
phenotypeLabel	Character string indicating the name of the binary covariate
esetList	An object of class ExpressionSetList
...	Not implemented. Potentially additional arguments to the above methods that are implemented in other packages

Details

This function is a wrapper that provides an estimate of effect size for each study (element) in an ExpressionSetList object.

For Welch t-statistic, this function is a wrapper for mt.teststat in the multtest package.

For SAM, this function is a wrapper for the sam function in the siggenes package.

The "z" statistic is a standardized unbiased estimate of effect size (Hedges and Olkin, 1985) – implementation is in the zScores function in the R package GeneMeta.

See the complete references below.

Value

A matrix: rows are genes and columns are studies

Author(s)

R. Scharpf

References

J.K. Choi, U. Yu, S. Kim, and O.J. Yoo (2003), Combining multiple microarray studies and modeling interstudy variation, Bioinformatics, 19(1) I84-I90.

Y. Ge, S. Dudoit & T. P. Speed (2003), Resampling-based multiple testing for microarray data hypothesis Test 12(1) : 1-44 (with discussions on 44-77).

L. Lusa R. Gentleman, and M. Ruschhaupt, GeneMeta: MetaAnalysis for High Throughput Experiments

L.V. Hedges and I. Olkin, Statistical Methods for Meta-analysis (1985), Academic Press

Tusher, Tibshirani and Chu (2001), Significance analysis of microarrays applied to the ionizing radiation response, PNAS 2001 98: 5116-5121, (Apr 24).

Examples

data(expressionSetList)
if(require(siggenes)){
  sam <- ssStatistic("sam", esetList=expressionSetList, phenotypeLabel="adenoVsquamous")
}  

XDE documentation built on Nov. 8, 2020, 5:02 p.m.