plotMA-methods {beadarray} | R Documentation

## Function to construct the classic MA plots from a dataset

### Description

Note that a ggplot2 object is returned, which can be modified programatically.

The default operation is to construct a reference array be averaging all probes across the whole datasets, and then making an MA plot by comparing each array to this reference. A log2 transformation is performed, but this can be turned-off by setting `do.log=FALSE`.

Alternatively, a SampleGroup may be specified. This is a character string that should match a column in the phenoData for the object. Then, the resulting MA plot will contain all pairwise comparisons between samples belonging to the same group. A list of ggplot objects is returned, each item in the list being a different group.

### Details

Densities are computed using the 'hexbin' package

### Value

A list of ggplot2 objects is returned.

### Author(s)

Mark Dunning

### Examples

    if(require(beadarrayExampleData)){
    library(ggplot2)
    data(exampleSummaryData)
    rawdata <- channel(exampleSummaryData, "G")
     mas <- plotMA(rawdata,do.log=FALSE)
    mas
    ##Smoothed lines can be added
    mas + geom_smooth(col="red")
    ##Added lines on the y axis
    mas + geom_hline(yintercept=c(-1.5,1.5),col="red")
    ##Changing the color scale
    mas + scale_fill_gradient2(low="yellow",mid="orange",high="red")

    mas <- plotMA(rawdata,do.log=FALSE,SampleGroup="SampleFac")

    ## Not run:
    mas[[1]]
    mas[[2]]

    ## End(Not run)

    }

[Package beadarray version 2.34.0 Index]