GeneSelector (version 2.22.0)

RankingFoxDimmic: Ranking based on the t-statistic of Fox and Dimmic

Description

Performs a two-sample Bayesian t test on a gene expression matrix using the method of Fox and Dimmic (2006).

Usage

RankingFoxDimmic(x, y, type = "unpaired", m = 4, 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

"unpaired":

two-sample test, equal variances assumed.

"paired" and "unpaired" are not possible for this kind of test.

m

The number of similarly expressed genes to use for calculating Bayesian variance and prior degrees of freedom. The default value suggested by Fox and Dimmic is currently 4, s. note.

pvalues

Should p-values be computed ? Default is TRUE.

gene.names

An optional vector of gene names.

...

Currently unused argument.

Value

GeneRanking.

References

Fox, R.J., Dimmic, M.W. (2006). A two sample Bayesian t-test for microarray data. BMC Bioinformatics, 7:126

See Also

RepeatRanking, RankingTstat, RankingFC, RankingWelchT, RankingWilcoxon, RankingBaldiLong, RankingLimma, RankingEbam, RankingWilcEbam, RankingSam, RankingShrinkageT, RankingSoftthresholdT, RankingPermutation

Examples

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