mboxplot-methods: Box Plots of Relative M Values
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Arguments Details Note Author(s) See Also Examples

Produce boxplots of relative M values for the set of arrays.

Usage

mboxplot(x, which = "", size = 0, transfo = log2, method = "mean", range = 0, ylim = c(-1,1), outline = FALSE, names = "namepart", ...)

`x`	object of class `DataTreeSet` or `ExprTreeSet`.
`which`	type of probes to be used, for details see `validData`.
`size`	length of sequence to be generated as subset.
`transfo`	a valid function to transform the data, usually “log2”, or “0”.
`method`	method to create the reference data, “mean” or “median”.
`range`	determines how far the plot whiskers extend out from the box.
`ylim`	range for the plotted y values.
`outline`	if `outline` is not true, the outliers are not drawn.
`names`	optional vector of sample names.
`...`	optional arguments to be passed to `boxplot`.

Create boxplots of M plots, where M is determined relative to a pseudo-mean 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.

For a DataTreeSet object, data must first be attached using method attachInten.

Christian Stratowa

mvaplot, boxplot

# load existing ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

# need to attach scheme mask and probe intensities
data.test3 <- attachMask(data.test3)
data.test3 <- attachInten(data.test3)

if (interactive()) {
mboxplot(data.test3, ylim=c(-6,6))
}

# optionally remove mask and data to free memory
data.test3 <- removeInten(data.test3)
data.test3 <- removeMask(data.test3)