sigint.plot {OLIN} | R Documentation

## Visualisation of significance of intensity-dependent bias

### Description

This function visualises the significance of intensity-dependent bias.

### Usage

    sigint.plot(A,M,Sp,Sn,ylim=c(-3,-3),...)

### Arguments

`A` | vector of average logged spot intensity
`M` | vector of logged fold changes
`Sp` | vector of false discovery rate or p-values for positive deviation of median/mean of \code{M} as produced by `fdr.int` or `p.int`
`Sn` | vector of false discovery rate or p-values for negative deviation of median/mean of \code{M} as produced by `fdr.int` or `p.int`
`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.plot` produces a MA-plot of the significance (`Sp`,`Sn`) generated by `fdr.int` or `p.int`. The abscissa (x-axis) is shows by the average logged spot intensity `A=0.5*(log(Cy3)+log(Cy5))`; the ordinate axis (y-axis) shows the log10(FDR) or log10(p) given by `FDRp` or `Pn` and `FDRn` or `Pn`. The significance for positive median/mean of \code{M} of spot intensity neighbourhoods are presented by red colour; the significance for negative median/mean of \code{M} of spot intensity neighbourhoods are presented by green colour. The ordinate axis (y-axis) give the log10-transformed FDR or p-values.

### Author(s)

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

### See Also

`sigxy.plot`, `fdr.int`, `p.int`

### Examples

    # To run these examples, "un-comment" them!
    #
    # LOADING DATA NOT-NORMALISED
    # data(sw)
    # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
    # This can take a while! For testing, you may choose a smaller N.
    # FDR <- fdr.int(maA(sw)[,1],maM(sw)[,1],delta=50,N=100,av="median")
    # VISUALISATION OF RESULTS
    # sigint.plot(maA(sw)[,1],maM(sw)[,1],FDR$FDRp,FDR$FDRn,c(-5,-5))

    # data(sw.olin)
    # CALCULATION OF SIGNIFICANCE OF SPOT NEIGHBOURHOODS
    # F <- fdr.int(maA(sw.olin)[,1],maM(sw.olin)[,1],delta=50,N=100,av="median")
    # VISUALISATION OF RESULTS
    # sigint.plot(maA(sw.olin)[,1],maM(sw.olin)[,1],FDR$FDRp,FDR$FDRn,c(-5,-5))

[Package OLIN version 1.64.0 Index]