RankingBstat {GeneSelector} | R Documentation

## Ranking based on the B-statistic

### Description

The B-statistic was motivated in a bayesian framework described by Lonnstedt and Speed (2002). It is implemented in the package `sma`, the function is just a wrapper.
For `S4` method information, see RankingBstat-methods.

### Usage

    RankingBstat(x, y, type = c("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` | "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. `"unpaired"` is not possible.
`gene.names` | An optional vector of gene names.
`...` | Furher arguments passed to `stat.bayesian` from the package `sma`

### Value

An object of class GeneRanking.

### Author(s)

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

### References

Lonnstedt, I., Speed, T. (2002).
Replicated microarray data. Statistica sinica, 12, 31-46

### See Also

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

### Examples

    ## Load toy gene expression data
    data(toydata)
    ### class labels
    yy <- toydata[1,]
    ### gene expression
    xx <- toydata[-1,]
    ### run RankingBstat
    Bstat <- RankingBstat(xx, yy, type="paired")

[Package GeneSelector version 1.2.0 Index]