# Calibration model for estimating absolute expression levels from microarray data

## Documentation for package ‘CALIB’ version 1.10.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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