MicroarrayData: The MicroarrayData class

Description Fields and Methods Author(s)


Package: aroma
Class MicroarrayData


Directly known subclasses:
BMAData, GenePixData, ImaGeneData, MAData, QuantArrayData, RawData, RGData, ScanAlyze20Data, ScanAlyzeData, SpotData, SpotfinderData, TMAData

public static class MicroarrayData
extends Object

This class is abstract can not be instanciated.

Fields and Methods


layout The layout structure of the microarray slide(s).


append Appends another MicroarrayData object.
applyGenewise -
applyGroupwise -
applyPlatewise -
applyPrintdipwise -
applyPrinttipwise -
as.character -
as.data.frame Converts the object to a data frame.
boxplot Plots a boxplot.
clearCache -
equals Compares a MicroarrayData object with another Object.
extract Gets a subset of data specified by fields, slides and/or spot indices.
getBlank -
getCache -
getChannelNames Gets the names of the channels.
getColors -
getExtreme -
getInclude -
getLabel Gets the label of one field.
getLayout Gets the layout.
getProbeWeights -
getSignalWeights -
getSlideNames Gets the names of the slides.
getSlidePairs -
getSpotPosition -
getSpotValue -
getTreatments -
getView -
getWeights -
getWeightsAsString -
hasLayout Checks if the layout has been specified.
hasProbeWeights -
hasSignalWeights -
hasWeights -
highlight Highlight spots in last plot.
hist Plots a histogram.
isFieldColorable -
keepSlides Remove all but the specified slides.
keepSpots Remove all but the specified spots from all slides.
lowessCurve Draws one or more lowess curves through the data in last plot.
nbrOfDataPoints -
nbrOfFields Gets the number of fields.
nbrOfSlides Gets the number of slides.
nbrOfSpots Gets the number of spots in each of the slides.
nbrOfTreatments -
normalizePlatewise Normalization performed plate by plate.
normalizePrintorder -
normalizeQuantile -
plot Plots spatial representation of a microarray spot statistics.
plotDensity Plots the empirical density distribution of a field.
plotGene -
plotPrintorder Plots the data as a time series in the order it was printed.
plotReplicates -
plotSpatial Plots a spatial representation of one field.
plotSpatial3d Plots a 3-dimensional spatial representation of a field.
plotXY Plots a scatter plot of two fields.
points -
qqnorm -
quantile -
range -
range2 -
read Reads microarray data generated by another software package.
readHeader -
removeSlides Remove specified slides.
removeSpots Remove specified spots.
resetProbeWeights -
resetSignalWeights -
select Selects rows with certain criteria.
seq -
setCache -
setLabel Sets the label of one field.
setLayout Sets the layout.
setProbeWeights Sets probe weights on one or several slides.
setSignalWeights -
setSlideNames Sets the names of the slides.
setTreatments -
setView -
setWeights -
size Gets the number of spots in all slides together.
str Compactly Display the Structure of a MicroarrayData object.
subplots Prepare for a grid of subplots based on the number of slides.
summary Gets summary statistics for the fields.
text Puts labels to the spots in last plot.
updateHeader -
validateArgumentChannel -
validateArgumentChannels -
validateArgumentGroupBy Validates the argument 'groupBy'.
validateArgumentWeights Validates the argument 'weights'.
write Write a MicroarrayData object to file.
writeHeader -

Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstanciationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save


Henrik Bengtsson (http://www.braju.com/R/)

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.