image-methods: Display an Image

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Creates an image of intensities or residuals, respectively, for each sample.

Usage

image(x, bg = FALSE, transfo = log2, col = NULL, names = "namepart", xlab = "", ylab = "", add.legend = FALSE, ...)

image(x, type = c("resids", "pos.resids", "neg.resids", "sign.resids", "weights"), qualopt = c("raw", "adjusted", "normalized"), transfo = log2, col = NULL, names = "namepart", xlab = "", ylab = "", add.legend = FALSE, ...)

Arguments

x	object of class ProcesSet.
bg	logical. If FALSE, intensities from slot data will be used; if TRUE, background intensities from slot bgrd will be used.
type	character string specifying the type of residual image.
qualopt	character string specifying whether to draw residual image for “raw”, “adjusted”, or “normalized” intensities.
transfo	a valid function to transform the data, usually “log2”, or “0”.
col	color range for intensities.
names	optional vector of sample names.
xlab	a label for the x axis.
ylab	a label for the y axis.
add.legend	logical, if TRUE then a color bar will be drawn.
...	optional arguments to be passed to image.

Details

Creates an image of intensities or residuals, respectively, for each array, i.e. ‘pseudo chip images’.

If x belongs to class DataTreeSet then images of raw intensities will be drawn.

If x belongs to class ExprTreeSet and bg=FALSE then images of background corrected intensities will be drawn.

If x belongs to class ExprTreeSet and bg=TRUE the distribution of the background intensities will be shown; this can be useful to see potential density gradients caused by hybridization conditions. For the computation of background intensities see function bgcorrect; it is suggested to use bgcorrect.mas4 to identify density gradients.

If x belongs to class QualTreeSet then images of the residuals or the probe weights, respectively, will be drawn. For col=NULL the same colors will be used as described in vignette “QualityAssess.pdf” of package affyPLM, using internally function pseudoPalette described in affyPLM.

For names=NULL full tree names will be displayed while for names="namepart" column names will be displayed without name extension. If names is a vector of tree names then data from these trees only will displayed as image(s).

Author(s)

Christian Stratowa

See Also

plotImage

Examples

## Not run: 
## images of raw intensities as imported using import.data()
unlist(treeNames(data.test3)) # show available tree names
image(data.test3, names="TestA2.cel")
image(data.test3)

## images of background adjusted or background intensities, created by e.g. rma()
getTreeNames(rootFile(data.rma))
image(data.rma, names="TestA2.int")
image(data.rma, names="TestA2.rbg", bg=TRUE)

## residual images, created by e.g. rmaPLM()
getTreeNames(rootFile(rlm.all), treetype="res")
image(rlm.all, type="resids")
image(rlm.all, type="resids", names="TestA2_raw.res", add.legend=TRUE)
image(rlm.all, type="pos.resids", names="TestA2_raw.res", add.legend=TRUE)
image(rlm.all, type="neg.resids", names="TestA2_raw.res", add.legend=TRUE)
image(rlm.all, type="sign.resids", names="TestA2_raw.res", add.legend=TRUE)
image(rlm.all, type="weights", names="TestA2_raw.res", add.legend=TRUE)
image(rlm.all, type="resids", qualopt="adjusted", names="TestA2_adjusted.res", add.legend=TRUE)

## End(Not run)

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