Calibration model for estimating absolute expression levels from microarray data


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Documentation for package ‘CALIB’ version 1.8.0

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adjustP2 Adjust model parameter P2
calibReadMe View CALIB readme file
cbind.ParameterList Combine RGList_CALIB, SpikeList or ParameterList objects
cbind.RGList_CALIB Combine RGList_CALIB, SpikeList or ParameterList objects
cbind.SpikeList Combine RGList_CALIB, SpikeList or ParameterList objects
coerce,RGList_CALIB,exprSet2-method Red, Green Intensity List - Class
dim.RGList_CALIB Retrieve the Dimensions of an RGList_CALIB or SpikeList object
dim.SpikeList Retrieve the Dimensions of an RGList_CALIB or SpikeList object
dimnames.RGList_CALIB Retrieve the Dimension Names of an RGList_CALIB or SpikeList object.
dimnames.SpikeList Retrieve the Dimension Names of an RGList_CALIB or SpikeList object.
estimateParameter Estimate model parameter from spikes
getColClasses Construct colClasses vector for use within read.rg function
length.RGList_CALIB Retrieve the Dimensions of an RGList_CALIB or SpikeList object
length.SpikeList Retrieve the Dimensions of an RGList_CALIB or SpikeList object
merge.RGList_CALIB Merge RGList_CALIB or SpikeList objects
merge.SpikeList Merge RGList_CALIB or SpikeList objects
normalizeData Normalization: estimation of absolute expression levels
normdata Example of normalized data
parameter Calibration Model parameter: ParameterList Example
ParameterList-class Class "ParameterList" - List to store all the parameters
plotNormalizedData plot estimated absolute levels of two conditions
plotSpikeCI plot spike concentration vs measured intensity
plotSpikeHI plot hybridized target vs intensity
plotSpikeRG plot spike intensity R vs G
plotSpikeSpotError plot spot error of spikes.
rbind.RGList_CALIB Combine RGList_CALIB, SpikeList or ParameterList objects
rbind.SpikeList Combine RGList_CALIB, SpikeList or ParameterList objects
read.rg Read RGList_CALIB from Image Analysis Output Files
read.spike Read SpikeList from a RGList_CALIB and Concentration files
RG Experiment Data: RGList_CALIB Example
RGList_CALIB-class Red, Green Intensity List - Class
show,ParameterList-method Class "ParameterList" - List to store all the parameters
show,RGList_CALIB-method Red, Green Intensity List - Class
show,SpikeList-method Class "SpikeList" - Spike Intensity and Concentration List
spike Experiment Data: SpikeList Example
SpikeList-class Class "SpikeList" - Spike Intensity and Concentration List
[.ParameterList Subset of RGList_CALIB, SpikeList or ParameterList object
[.RGList_CALIB Subset of RGList_CALIB, SpikeList or ParameterList object
[.SpikeList Subset of RGList_CALIB, SpikeList or ParameterList object