plotNUSE: Box Plots of Normalized Unscaled Standard Errors (NUSE) for...
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Author(s) See Also

Produce boxplot of Normalized Unscaled Standard Errors (NUSE) for the set of arrays and the selected device.

plotNUSE(x,
         which    = "UnitName",
         size     = 0,
         range    = 0,
         names    = "namepart",
         main     = "NUSE Plot",
         ylim     = c(0.8,1.2),
         las      = 2,
         add.line = TRUE,
         outline  = FALSE,
         dev      = "screen",
         outfile  = "NUSEPlot",
         w        = 800,
         h        = 540,
         ...)

`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.
`...`	optional arguments to be passed to `boxplot`.

Create boxplots of Normalized Unscaled Standard Errors (NUSE) for the set of arrays.

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.

Christian Stratowa

nuseplot

xps documentation built on Nov. 8, 2020, 6 p.m.