plot-methods: Plot of a ExpressionSet object

Description Usage Arguments Details See Also Examples

Description

Creating quality control plots of a ExpressionSet object

Usage

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## 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:

See Also

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

Examples

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## 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')

lumi documentation built on Nov. 17, 2017, 8:58 a.m.

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