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CALIB (version 1.38.0)

Calibration model for estimating absolute expression levels from microarray data

Description

This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.

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Version

Version

1.38.0

License

LGPL

Maintainer

Hui Zhao

Last Published

February 15th, 2017

Functions in CALIB (1.38.0)

plotSpikeHI

plot hybridized target vs intensity
spike

Experiment Data: SpikeList Example
read.spike

Read SpikeList from a RGList\_CALIB and Concentration files
cbind

Combine RGList\_CALIB, SpikeList or ParameterList objects
dim

Retrieve the Dimensions of an RGList\_CALIB or SpikeList object
normdata

Example of normalized data
read.rg

Read RGList\_CALIB from Image Analysis Output Files
merge

Merge RGList\_CALIB or SpikeList objects
plotSpikeRG

plot spike intensity R vs G
estimateParameter

Estimate model parameter from spikes
SpikeList-class

Class "SpikeList" - Spike Intensity and Concentration List
getColClasses

Construct colClasses vector for use within read.rg function
plotSpikeSpotError

plot spot error of spikes.
subsetting

Subset of RGList\_CALIB, SpikeList or ParameterList object
RG

Experiment Data: RGList\_CALIB Example
calibReadMe

View CALIB readme file
plotNormalizedData

plot estimated absolute levels of two conditions
RGList_CALIB-class

Red, Green Intensity List - Class
dimnames

Retrieve the Dimension Names of an RGList\_CALIB or SpikeList object.
parameter

Calibration Model parameter: ParameterList Example
ParameterList-class

Class "ParameterList" - List to store all the parameters
plotSpikeCI

plot spike concentration vs measured intensity
adjustP2

Adjust model parameter P2
normalizeData

Normalization: estimation of absolute expression levels