Box Plots of Relative Log Expression (RLE) for Device

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Description

Produce boxplot of Relative Log Expression (RLE) for the set of arrays and the selected device.

Usage

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plotRLE(x,
        which    = "UnitName",
        size     = 0,
        range    = 0,
        names    = "namepart",
        main     = "RLE Plot",
        ylim     = c(-1.0, 1.0),
        las      = 2,
        add.line = TRUE,
        outline  = FALSE,
        dev      = "screen",
        outfile  = "RLEPlot",
        w        = 800,
        h        = 540,
        verbose  = TRUE,
        ...) 

Arguments

x

object of class ExprTreeSet or QualTreeSet.

which

type of probes to be used, for details see validData.

size

length of sequence to be generated as subset.

range

determines how far the plot whiskers extend out from the box.

names

optional vector of sample names.

main

the main title for the plot.

ylim

range for the plotted y values.

las

the style of axis labels.

add.line

logical, if TRUE a horizontal line is drawn.

outline

if outline is not true, the outliers are not drawn.

dev

graphics device to plot to, i.e. one of “screen”, “jpeg”,“png”, “pdf” or “ps”.

outfile

the name of the output file.

w

the width of the device in pixels.

h

the height of the device in pixels.

verbose

logical, if TRUE print status information.

...

optional arguments to be passed to boxplot.

Details

Create boxplots of Relative Log Expression (RLE) values for the set of arrays, i.e. of M plots, where M is determined relative to a pseudo-median reference chip.

For names=NULL full column names of slot data will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of column names, only these columns will displayed as boxplot.

Author(s)

Christian Stratowa

See Also

rleplot

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