sigint.plot2 {OLIN} | R Documentation

## Visualisation of significance of intensity-dependent bias

### Description

This function produce visualises the significance of intensity-dependent bias.

### Usage

    sigint.plot2(object,Sp,Sn,ylim=c(-3,-3),...)

### Arguments

`object` | object of class marrayRaw or marrayNorm
`Sp` | vector of false discovery rate or p-values for positive deviation of median/mean of \code{M} as produced by `fdr.int2` or `p.int2`
`Sn` | vector of false discovery rate or p-values for negative deviation of median/mean of \code{M} as produced by `fdr.int2` or `p.int2`
`ylim` | vector of minimal log10(fdr) or log10(p-value) to be visualised corresponding to `Sp` and `Sn`. FDR or p-values smaller than these values will be set equal to these threshold values for visualisation.
`...` | Further optional graphical parameter for the `plot` function generating the MA plot

### Details

The function `sigint.plot2` only differs from `sigint.plot` in its input arguments. The functionality is the same. For details, see `sigint.plot`.

### Note

This function will be merged with `sigint.plot` in future versions.

### Author(s)

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

### See Also

`sigxy.plot`, `fdr.int2`, `p.int2`

### 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 1.70.0 Index]