visualiseHybridisations {arrayMagic} | R Documentation |
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
.
visualiseHybridisations(arrayDataObject, exprSetRGObject, type="raw", hybridisations, slideNameColumn, numberOfSpots, nrOfBlocksPerRow=4, mappingColumns= list(Block="Block", Column="Column", Row="Row"), transFunc=log, savePath=".", plotOutput="pdf")
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" |
None, but a plot is generated.
Andreas Buness <a.buness@dkfz.de>
spatialLayout
,
exprSetRG-class
,
arrayData-class