bg.adjust.affinities
(Package: gcrma) :
Background adjustment with sequence information (internal function)
An internal function to be used by gcrma.
● Data Source:
BioConductor
● Keywords: manip
● Alias: bg.adjust.affinities, bg.adjust.constant, bg.adjust.fullmodel, bg.adjust.mm, bg.adjust.optical
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bg.adjust.gcrma
(Package: gcrma) :
GCRMA background adjust (internal function)
This function performs background adjustment (optical noise and non-specific binding on an AffyBatch project and returns an AffyBatch object in which the PM intensities are adjusted.
● Data Source:
BioConductor
● Keywords: manip
● Alias: bg.adjust.gcrma
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0 images
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bg.parameters.ns
(Package: gcrma) :
Estimation of non-specific Binding Background Parameters
An internal function to be used by gcrma
● Data Source:
BioConductor
● Keywords: manip
● Alias: PAV, average.for.PAV, bg.parameters.ns, left.sigma
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0 images
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An internal function to calculate probe affinities from their sequences.
● Data Source:
BioConductor
● Keywords: manip
● Alias: base.profiles, base.profiles.mm, base.profiles.nc, check.probes, compute.affinities, compute.affinities.local, compute.affinities2, compute.affinity.coef, plotBaseProfiles
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fast.bkg
(Package: gcrma) :
Internal functions for justGCRMA
These are internal functions for justGCRMA that are called based on memory or speed constraints.
● Data Source:
BioConductor
● Keywords: internal
● Alias: fast.bkg, mem.bkg
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0 images
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gcrma
(Package: gcrma) :
Robust Multi-Array expression measure using sequence information
This function converts an AffyBatch into an ExpressionSet using the robust multi-array average (RMA) expression measure with help of probe sequence.
● Data Source:
BioConductor
● Keywords: manip
● Alias: GSB.adj, gcrma, gcrma.bg.transformation, gcrma.bg.transformation.fast
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0 images
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gcrma.engine
(Package: gcrma) :
GCRMA background adjust engine(internal function)
This function adjust for non-specific binding when all arrays in the dataset share the same probe affinity information. It takes matrices of PM probe intensities, MM probe intensities, other negative control probe intensities(optional) and the associated probe affinities, and return one matrix of non-specific binding corrected PM probe intensities.
● Data Source:
BioConductor
● Keywords: manip
● Alias: gcrma.engine
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0 images
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gcrma.engine2
(Package: gcrma) :
GCRMA background adjust engine(internal function)
This function adjust for non-specific binding when each array has its own probe affinity information. It takes an AffyBatch object of probe intensities and an AffyBatch of probe affinity, returns one matrix of non-specific binding corrected PM probe intensities.
● Data Source:
BioConductor
● Keywords: manip
● Alias: gcrma.engine2
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0 images
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getCDF
(Package: gcrma) :
Functions for Automatic Download of Packages
These are internal functions that are called by justGCRMA and GCRMA in order to automatically download and install cdf environments and probe packages.
● Data Source:
BioConductor
● Keywords: internal
● Alias: getCDF, getProbePackage
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0 images
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justGCRMA
(Package: gcrma) :
Compute GCRMA Directly from CEL Files
This function converts CEL files into an ExpressionSet using the robust multi-array average (RMA) expression measure with help of probe sequences.
● Data Source:
BioConductor
● Keywords: manip
● Alias: just.gcrma, justGCRMA
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0 images
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