processArrayDataObject {arrayMagic} | R Documentation |
Automated processing and normalisation of an
arrayData
-object.
The function is called
by processArrayData
.
processArrayDataObject(arrayDataObject, spotIdentifier = "Name", verbose = TRUE, normalisationMethod = "vsn", subtractBackground=FALSE, spotsRemovedBeforeNormalisation = NULL, spotsRemovedAfterNormalisation = NULL, subGroups = NULL, channelsSeparately = FALSE, hybridisationGroups = NULL)
arrayDataObject |
object of class arrayData-class ;
required; default missing
|
spotIdentifier |
character string; required; default "Name".
spotIdentifier specifies the column
in the image analysis result files which contain
spot or gene identifiers. |
verbose |
logical; required; default: TRUE |
normalisationMethod |
character string; required; default: "vsn";
cf. argument method of normalise |
subtractBackground |
logical; required; default: FALSE
cf. normalise |
spotsRemovedBeforeNormalisation |
vector of character strings;
required; default NULL .
All spots which match the string(s) will be excluded
already before normalisation and will not be present
in the resulting objects at all.
|
spotsRemovedAfterNormalisation |
vector of character strings;
required; default: NULL ;
cf. argument spotsRemovedBeforeNormalisation
|
subGroups |
character string or NULL ;
required; cf. normalise ;
default: NULL |
channelsSeparately |
logical; required;
cf. normalise ;
default: FALSE |
hybridisationGroups |
list of numeric vectors;
cf. normalise ;
required; default: NULL |
A list of objects, i.e. an "exprSetRGObject" and
"arrayDataObject"
with corresponding class types
exprSetRG-class
,
arrayData-class
.
Andreas Buness <a.buness@dkfz.de>
processArrayData
,
normalise
,
exprSetRG-class
,
arrayData-class
LOADPATH <- file.path(.path.package("arrayMagic"), "extdata") SLIDEDESCRIPTIONFILE <- "slideDescription" slideDescription <- readpDataSlides( loadPath=LOADPATH, slideDescriptionFile=SLIDEDESCRIPTIONFILE ) arrayDataObject <- readIntensities( loadPath=LOADPATH, slideDescription=slideDescription ) resultList <- processArrayDataObject( arrayDataObject=arrayDataObject )