plot-methods {lumi} | R Documentation

## Plot of a ExpressionSet object

### Description

Creating quality control plots of a ExpressionSet object

### Usage

    ## S4 method for signature 'ExpressionSet,missing'
    plot(x, what = c("density", "boxplot", "pair", "MAplot", "sampleRelation", "outlier", "cv"), main, ...)

### Arguments

`x` | a ExpressionSet object returned by `lumiQ`
`what` | one of the six kinds of QC plots
`main` | the title of the QC plot
`...` | additional parameters for the corresponding QC plots

### Details

The parameter "what" of `plot` function controls the type of QC plots, which includes:

- density: the density plot of the chips, see `hist-methods`

- boxplot: box plot of the chip intensities, see `boxplot-methods`

- pair: the correlation among chips, plot as a hierarchical tree, see `pairs-methods`

- MAplot: the MAplot between chips, see `MAplot-methods`

- sampleRelation: plot the sample relations. See `plotSampleRelation`

- outlier: detect the outliers based on the sample distance to the center. See `detectOutlier`

- cv: the density plot of the coefficients of variance of the chips. See `estimateLumiCV`

### See Also

`LumiBatch-class`, `hist-methods`, `boxplot-methods`, `MAplot-methods`, `pairs-methods`, `plotSampleRelation`, `estimateLumiCV`, `detectOutlier`

### Examples

    ## load example data
    data(example.lumi)

    ## Quality control estimation
    lumi.Q <- lumiQ(example.lumi)

    ## summary
    summary(lumi.Q)

    ## plot the density
    plot(lumi.Q, what='density')

    ## plot the pairwise sample correlation
    plot(lumi.Q, what='pair')

    ## plot the pairwise MAplot
    plot(lumi.Q, what='MAplot')

    ## sample relations
    plot(lumi.Q, what='sampleRelation', method='mds', color=c('100US', '95US:5P', '100US', '95US:5P'))

    ## detect outlier based on the distance to the mean profile
    plot(lumi.Q, what='outlier')

    ## Density plot of coefficient of variance
    plot(lumi.Q, what='cv')

[Package lumi version 2.40.0 Index]