fdr.int2 {OLIN} | R Documentation

## Assessment of the significance of intensity-dependent bias

### Description

This function assesses the significance of intensity-dependent bias by an one-sided random permutation test. The observed average values of logged fold-changes within an intensity neighbourhood are compared to an empirical distribution generated by random permutation. The significance is given by the false discovery rate.

### Usage

    fdr.int2(object,delta=50,N=100,av="median")

### Arguments

`object` | object of class marrayRaw or marrayNorm
`delta` | integer determining the size of the neighbourhood. The actual window size is (`2 * delta+1`).
`N` | number of random permutations performed for generation of empirical distribution
`av` | averaging of `M` within neighbourhood by mean or median (default)

### Details

This function `fdr.int2` is basically the same as `fdr.int` except for differences in their in- and output format. For the details about the functionality, see `fdr.int`.

### Note

This function will be merged with `fdr.int` in future versions.

### Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

### See Also

`fdr.int`, `p.int2`, `sigint.plot2`

### Examples

    # To run these examples, delete the comment signs (#) in front of the commands.
    #
    # LOADING DATA NOT-NORMALISED
    # data(sw)
    # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
    # For this example, N was chosen rather small. For "real" analysis, it should be larger.
    # FDR <- fdr.int2(sw,delta=50,N=10,av="median")
    # VISUALISATION OF RESULTS
    # sigint.plot2(sw[,1],FDR$FDRp[[1]],FDR$FDRn[[1]],c(-5,-5)) # array 1
    # sigint.plot2(sw[,4],FDR$FDRp[[4]],FDR$FDRn[[4]],c(-5,-5)) # array 4

[Package OLIN version 1.10.0 Index]