RankingFoxDimmic {GeneSelector} | R Documentation

## 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

An object of class GeneRanking.

### Note

Although the test of Fox and Dimmic is very similar to that of Baldi and Long; there are various slight differences, in particular with respect to the computation of the Bayesian variance.

### Author(s)

Martin Slawski
Anne-Laure Boulesteix

### 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")

[Package GeneSelector version 2.30.0 Index]