statFDR {sights} | R Documentation

## FDR control

### Description

Apply Storey's FDR control to p-values

### Usage

    statFDR(testMatrix, ctrlMethod = "smoother", ...)

### Arguments

`testMatrix` | Data frame or numeric matrix consisting of output from `statT` or `statRVM` functions. P-value columns from this matrix are automatically selected for FDR calculation. Columns are samples, and rows are plate wells.
`ctrlMethod` | Optional. Method to use either 'smoother' or 'bootstrap' to estimate null. Default is 'smoother'.
`...` | Optional. Additional parameters passed to `qvalue` function.

### Details

False Discovery Rate procedure is used to control the proportion of false positives in the results. This is an implementation of the positive false discovery (pFDR) procedure of the `qvalue` function.

### Value

A matrix of parameters for each replicate group is returned:

`T-statistic or RVM T-statistic` | Value of the t-statistic.
`Mean_Difference` | Difference between the calculated and the true mean.
`Standard_Error` | Standard error of the difference between means.
`Degrees_Of_Freedom` | Degrees of freedom for the t-statistic.
`P-value` | P-value for the t-test.
`q-value` | FDR q-value for the P-value.

### Note

Please install the package 'qvalue' from Bioconductor, if not already installed.

### References

Storey (2002). A direct approach to false discovery rates. Journal of the Royal Statistical Society: Series B, 64, 479-498.

### See Also

Other statistical methods: `statRVM`, `statT`

### Examples

    ## load dataset
    data(ex_dataMatrix)

    ## normalize data matrix using any method and store in new variable
    ex_normMatrix <- normSights(dataMatrix = ex_dataMatrix, dataCols = 5:10,
    normMethod = 'normZ')
    ## test normalized data matrix using either the RVM or T test and store in new variable
    ex_testMatrix <- statT(normMatrix = ex_normMatrix, trueMean = 0,
    repIndex = c(1,1,1,2,2,2))
    ## apply FDR control to test matrix with bootstrap control method
    ex_ctrlMatrix <- statFDR(testMatrix = ex_testMatrix,
    ctrlMethod = 'bootstrap')

[Package sights version 1.12.0 Index]