RankingWelchT {GeneSelector}R Documentation

Ranking based on the Welch t statistic.

Description

Performs univariate (rowwise) Welch tests on a gene expression matrix. The Welch t statistic is a better alternative to the 'ordinary' t statistic in the two sample, unequal variances setting.
For S4 method information, see RankingWelchT-methods.

Usage

RankingWelchT(x, y, type = "unpaired", pvalues = TRUE, gene.names = NULL, ...)

Arguments

x A matrix of gene expression values with rows corresponding to genes and columns corresponding to observations or alternatively an object of class ExpressionSet.
y If x is a matrix, then y may be a numeric vector or a factor with at most two levels.
If x is an ExpressionSet, then y is a character specifying the phenotype variable in the output from pData.
type Only the two sample case, type="unpaired" is possible. Otherwise, use RankingTstat. Variances are assumed to be unequal.
pvalues Should p-values be computed ? Default is TRUE.
gene.names An optional vector of gene names.
... Currenly unused argument.

Value

An object of class GeneRanking.

Author(s)

Martin Slawski martin.slawski@campus.lmu.de
Anne-Laure Boulesteix http://www.slcmsr.net/boulesteix

See Also

GetRepeatRanking, RankingTstat, RankingFC, RankingWilcoxon, RankingBaldiLong, RankingFoxDimmic, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingBstat, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation, RankingGap

Examples

## Load toy gene expression data
data(toydata)
### class labels
yy <- toydata[1,]
### gene expression
xx <- toydata[-1,]
### run RankingWelch
welchT <- RankingWelchT(xx, yy, type="unpaired")

[Package GeneSelector version 1.4.0 Index]