visualiseHybridisations {arrayMagic}R Documentation

Microarray intensity data are visualised with respect to their spatial layout

Description

Two colour microarray intensity data are visualised with respect to their spatial layout. Missing values (NA) as well as minus infinity (-Inf) etc. are not visualised. They appear to be white, i.e. in the colour of the background. -Inf might be a result of the (log-)transformation of the data; cf. the argument transFunc.

Usage

visualiseHybridisations(arrayDataObject, exprSetRGObject, type="raw", hybridisations, slideNameColumn, numberOfSpots, nrOfBlocksPerRow=4, mappingColumns= list(Block="Block", Column="Column", Row="Row"), transFunc=log, savePath=".", plotOutput="pdf")

Arguments

arrayDataObject object of class arrayData; required; default: missing
exprSetRGObject object of class exprSetRG; only required, if type = "normalised" or type = "normalisedLogRatio"; default: missing
type vector of character strings; required; default "raw"; valid strings are "raw", "rawLogRatio", "rawLogRatioBackgroundSubtracted", "normalised" or "normalisedLogRatio"
hybridisations vector of integers; optional; default: missing, i.e. all microarray slides
slideNameColumn character string specifying the column getHybAttr(arrayDataObject) which contains the names of the hybridisations; optional; default: missing
numberOfSpots integer; optional; default: missing; but required if the values in arrayDataObject do not cover the whole microarray slide, i.e. do not contain all spots; cf. spatialLayout.
nrOfBlocksPerRow integer; cf. spatialLayout; required; default: 4
mappingColumns list; required; the list elements named "Block", "Column", "Row" define the corresponding column names given in getSpotAttr(arrayDataObject); the "Block" element is optional, if missing a single block is assumed; default: list(Block="Block", Column="Column", Row="Row"); cf. spatialLayout
transFunc transformation function applied to the raw data, in particular in combination with type = "raw" you may for example use log or rank; (note: type = "rawLogRatio" and type = "rawLogRatioBackgroundSubtracted" require log ); required; default: log
savePath character string; required; default: "."
plotOutput character string; required; either "screen", "pdf" or "win.metafile"; default: "pdf"

Value

None, but a plot is generated.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

spatialLayout, exprSetRG-class, arrayData-class

Examples

        

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