# Graphics Toolbox for Assessment of Affymetrix Expression Measures

## Documentation for package ‘affycomp’ version 1.22.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

affycomp | Assessment functions
affycomp.compfig2 | Auxiliary functions to create comparitive Figures
affycomp.compfig2b | Auxiliary functions to create comparitive Figures
affycomp.compfig3 | Auxiliary functions to create comparitive Figures
affycomp.compfig4a | Auxiliary functions to create comparitive Figures
affycomp.compfig4b | Auxiliary functions to create comparitive Figures
affycomp.compfig4c | Auxiliary functions to create comparitive Figures
affycomp.compfig5a | Auxiliary functions to create comparitive Figures
affycomp.compfig5b | Auxiliary functions to create comparitive Figures
affycomp.compfig5c | Auxiliary functions to create comparitive Figures
affycomp.compfig5cde | Auxiliary functions to create comparitive Figures
affycomp.compfig5d | Auxiliary functions to create comparitive Figures
affycomp.compfig5e | Auxiliary functions to create comparitive Figures
affycomp.compfig7 | SD Assessment Functions
affycomp.compfigs | Assessment Plots
affycomp.compfigs.auxiliary | Auxiliary functions to create comparitive Figures
affycomp.compfigs.calls | Assessment Plots
affycomp.figure.calls | Assessment Plots
affycomp.figure1 | Auxiliary functions to create Figures
affycomp.figure1b | Auxiliary functions to create Figures
affycomp.figure2 | Auxiliary functions to create Figures
affycomp.figure2b | Auxiliary functions to create Figures
affycomp.figure3 | Auxiliary functions to create Figures
affycomp.figure4a | Auxiliary functions to create Figures
affycomp.figure4b | Auxiliary functions to create Figures
affycomp.figure4c | Auxiliary functions to create Figures
affycomp.figure5a | Auxiliary functions to create Figures
affycomp.figure5b | Auxiliary functions to create Figures
affycomp.figure5c | Auxiliary functions to create Figures
affycomp.figure5d | Auxiliary functions to create Figures
affycomp.figure5e | Auxiliary functions to create Figures
affycomp.figure6a | Auxiliary functions to create Figures
affycomp.figure6b | Auxiliary functions to create Figures
affycomp.figure7 | SD Assessment Functions
affycomp.figures | Assessment Plots
affycomp.figures.auxiliary | Auxiliary functions to create Figures
affycompPlot | Assessment Plots
affycompTable | Expression Assessment Table
assessAll | Assessment functions
assessDilution | Assessment functions for Dilution Data
assessFC | Assessment functions for Spike In Data
assessFC2 | Assessment functions for Spike In Data
assessLS | New Assessment functions for Spike In Data
assessMA | Assessment functions for Spike In Data
assessMA2 | New Assessment functions for Spike In Data
assessSD | SD Assessment functions
assessSignal | Assessment functions for Spike In Data
assessSpikeIn | Assessment functions for Spike In Data
assessSpikeIn2 | New Assessment functions for Spike In Data
assessSpikeInSD | New Assessment functions for Spike In Data
dilution.phenodata | Phenotypic Information for Dilution Study
exprset.log | Take log base 2 of Expression
hgu133a.spikein.phenodata | phenotypic information for HGU133A spike in study
hgu133a.spikein.xhyb | Cross hybridizers
lw.sd.assessment | An example of the result of an SD assessment
mas5.assessment | An example of the result of the assessments
mas5.assessment.133 | An example of the result of the assessments
mas5.assessment2 | An example of the result of the assessments
mas5.assessment2.133 | An example of the result of the assessments
read.dilution | Read Expression Date Sets
read.newspikein | Read Expression Date Sets
read.spikein | Read Expression Date Sets
readin | Read Expression Date Sets
remove.hgu133a.xhyb | Remove crosshybridizers
rma.assessment | An example of the result of an assessment
rma.assessment.133 | An example of the result of an assessment
rma.assessment2 | An example of the result of an assessment
rma.assessment2.133 | An example of the result of an assessment
rma.sd.assessment | An example of the result of an SD assessment
SD | SD Assessment Functions
spikein.phenodata | phenotypic information for spike in study
tableAll | Expression Assessment Table
tableDilution | Expression Assessment Table
tableFC | Expression Assessment Table
tableFC2 | Expression Assessment Table
tableLS | Expression Assessment Table
tableMA2 | Expression Assessment Table
tableOverallSNR | Expression Assessment Table
tableRanks | Expression Assessment Table
tableSD | SD Assessment Functions
tableSignal | Expression Assessment Table
tableSpikeInSD | Expression Assessment Table