RankingShrinkageT {GeneSelector} | R Documentation

## Ranking based on the 'shrinkage t' statistic

### Description

The shrinkage t statistic stabilizes the estimated variances appearing in the denominator of the statistic via a James-Stein-Shrinkage approach (Opgen-Rhein and Strimmer,2007). In this implementation, the shrinkage target is the median of the variances.
For `S4` method information, see RankingShrinkageT-methods.

### Usage

    RankingShrinkageT(x, y, type = c("unpaired", "paired", "onesample"), 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`. If `type = paired`, the first half of the columns corresponds to the first measurements and the second half to the second ones. For instance, if there are 10 observations, each measured twice, stored in an expression matrix `expr`, then `expr[,1]` is paired with `expr[,11]`, `expr[,2]` with `expr[,12]`, and so on.
`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`. If `type = paired`, take care that the coding is analogously to the requirement concerning `x`
`type` | "unpaired": two-sample test. "paired": paired test. Take care that the coding of `y` is correct (s. above) "onesample": `y` has only one level. Test whether the true mean is different from zero.
`gene.names` | An optional vector of gene names.
`...` | Currently 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

### References

Opgen-Rhein, R., Strimmer, K. (2007).
Accurate Ranking of Differentially Expressed Genes by a Distribution-Free Shrinkage Approach. Statistical Applications in Genetics and Molecular Biology, Vol. 6, Iss. 1, Art.9

### See Also

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

### Examples

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

[Package GeneSelector version 1.4.0 Index]