calcAIC
(Package: stepNorm) :
Extract AIC from a Fitted Model
Computes the Akaike Information Criterion for a fitted parametric model.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calcAIC
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calcBIC
(Package: stepNorm) :
Extract BIC from a Fitted Model
Computes the Bayesian Information Criterion for a fitted parametric model.
● Data Source:
BioConductor
● Keywords: manip
● Alias: calcBIC
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fit2DWithin
(Package: stepNorm) :
Bivariate location normalization function for cDNA microarray data
This function performs 2D location normalization on cDNA micoroarray. It operates on class marrayRaw or class marrayNorm. It allows the user to choose from a set of four basic normalization procedures.
● Data Source:
BioConductor
● Keywords: models
● Alias: fit2DWithin
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fitWithin
(Package: stepNorm) :
Simple location normalization function for cDNA microarray data
This function performs location normalization on cDNA micoroarray. It operates on class marrayRaw or class marrayNorm. It allows the user to choose from a set of three basic normalization procedures.
● Data Source:
BioConductor
● Keywords: models
● Alias: fitWithin
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This function is a modification of the maCompPlate function in the marray library. It generates plate IDs from the dimensions of the grid and spot matrices. Unlike the maCompPlate function, the number of spots is not necessarily a multiple of the number of wells on a plate, therefore this function allows empty spots on the slide.
● Data Source:
BioConductor
● Keywords: manip
● Alias: maCompPlate2
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makeStepList
(Package: stepNorm) :
Construction of a stepwise normalization list
This function provides a user friendly way to construct a list for input to the function stepWithinNorm. The list indicates intended biases for correction and models for stepwise normalization.
● Data Source:
BioConductor
● Keywords: models
● Alias: makeStepList
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A simple list-based class for the storage of parameters and results of normalization of cDNA microarray data.
● Data Source:
BioConductor
● Keywords: classes
● Alias: marrayFit, marrayFit-class
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seqWithinNorm
(Package: stepNorm) :
Sequential within-slide normalization function
This function conducts cDNA microarray normalization in a sequential fashion. In a two-color cDNA array setting, within-slide normalization calibrates signals from the two channels to remove non-biological variation introduced by various processing steps.
● Data Source:
BioConductor
● Keywords: models
● Alias: seqWithinNorm
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Internal stepNorm functions.
● Data Source:
BioConductor
● Keywords: internal
● Alias: MedianSmooth, aov2Dfit, calcEnp, loess2Dfit, loessfit, medfit, noFit, rlm2Dfit, rlmfit, spatialMedfit, square
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stepWithinNorm
(Package: stepNorm) :
Stepwise within-slide normalization function
This function conducts cDNA microarray normalization in a stepwise fashion. In a two-color cDNA array setting, within-slide normalization calibrates signals from the two channels to remove non-biological variation introduced by various processing steps.
● Data Source:
BioConductor
● Keywords: models
● Alias: stepWithinNorm
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