Package: aroma.affymetrix
Class RmaBackgroundCorrection
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ProbeLevelTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--BackgroundCorrection
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--RmaBackgroundCorrection
Directly known subclasses:
public static class RmaBackgroundCorrection
extends BackgroundCorrection
This class represents the RMA background adjustment function.
RmaBackgroundCorrection(..., addJitter=FALSE, jitterSd=0.2, seed=6022007)
Arguments passed to the constructor of
BackgroundCorrection.
If TRUE, Zero-mean gaussian noise is added to the
signals before being background corrected.
Standard deviation of the jitter noise added.
An (optional) integer specifying a temporary random seed
to be used for generating the (optional) jitter. The random seed
is set to its original state when done. If NULL, it is not set.
Methods:
process | - |
Methods inherited from BackgroundCorrection:
getParameters, process
Methods inherited from ProbeLevelTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
Methods inherited from Object:
$, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, names, objectSize, print, save, asThis
The fitting algorithm of the RMA background correction model may not converge if there too many small and discrete signals. To overcome this problem, a small amount of noise may be added to the signals before fitting the model. This is an ad hoc solution that seems to work. However, add Gaussian noise may generate non-positive signals.
Ken Simpson, Henrik Bengtsson
Internally bg.adjust is used to background correct the
probe signals. The default is to background correct PM signals only.