# geneChip Analysis Package

## Documentation for package ‘ArrayTools’ version 1.8.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

A C D E G H I M O P Q R S

## -- A --

adjustment | Access the multiple comparison adjustment method from the regressResult or interactionResult class
adjustment-method | Class to Contain the Regression Result Based on An Interaction Model
adjustment-method | Class to Contain the Regression Result

## -- C --

class:contrastMatrix | Class to Contain the Contrast Matrix that Used for Linear Regression
class:designMatrix | Class to Contain the Design Matrix that Used for Linear Regression
class:interactionResult | Class to Contain the Regression Result Based on An Interaction Model
class:regressResult | Class to Contain the Regression Result
contrastMatrix | Class to Contain the Contrast Matrix that Used for Linear Regression
contrastMatrix-class | Class to Contain the Contrast Matrix that Used for Linear Regression
createExpressionSet | Creating an ExpressionSet
createGSEAFiles | A Wrapper Function to create *.GCT and *.CLS for GSEA analysis
createIndex | Creating an HTML index file
createIngenuityFile | A Wrapper Function to Create Files for Ingenuity Analysis

## -- D --

designMatrix | Class to Contain the Design Matrix that Used for Linear Regression
designMatrix-class | Class to Contain the Design Matrix that Used for Linear Regression

## -- E --

eSetExample | An ExpressionSet example
exprsExample | a data.frame contains expression data

## -- G --

geneFilter | filter an ExpressionSet using different methods
getAdjP | access the adjPVal slot from regressResult or interactionResult class
getAdjP-method | Class to Contain the Regression Result Based on An Interaction Model
getAdjP-method | Class to Contain the Regression Result
getAnnotation | access the annotation slot from the regressResult or interactionResult slot
getAnnotation-method | Class to Contain the Regression Result Based on An Interaction Model
getAnnotation-method | Class to Contain the Regression Result
getCompare1 | Access the Compare1 slot from the contrastMatrix
getCompare1-method | Class to Contain the Contrast Matrix that Used for Linear Regression
getCompare2 | Access the compare2 slot from the contrastMatrix class
getCompare2-method | Class to Contain the Contrast Matrix that Used for Linear Regression
getContrast | Access the contrast matrix from the contrastMatrix class
getContrast-method | Class to Contain the Contrast Matrix that Used for Linear Regression
getContrast-method | Class to Contain the Regression Result Based on An Interaction Model
getContrast-method | Class to Contain the Regression Result
getCovariates | Accessing the covariates from the designMatrix class
getCovariates-method | Class to Contain the Design Matrix that Used for Linear Regression
getDesign | Access the design matrix from the designMatrix class
getDesign-method | Class to Contain the Design Matrix that Used for Linear Regression
getF | access the foldChange slot from regressionResult or interactionResult class
getF-method | Class to Contain the Regression Result Based on An Interaction Model
getF-method | Class to Contain the Regression Result
getFC | Access the foldChange slot from the regressResult or interactionResult class
getFC-method | Class to Contain the Regression Result Based on An Interaction Model
getFC-method | Class to Contain the Regression Result
getFCCutoff | Access the significantFCCutoff slot from the regressResult or interactionResult class
getFCCutoff-method | Class to Contain the Regression Result Based on An Interaction Model
getFCCutoff-method | Class to Contain the Regression Result
getFileName-method | Class to Contain the Regression Result Based on An Interaction Model
getFileName-method | Class to Contain the Regression Result
getFilterMethod | Access the filterMethod slot from the regressResult or interactionResult class
getFilterMethod-method | Class to Contain the Regression Result Based on An Interaction Model
getFilterMethod-method | Class to Contain the Regression Result
getID | access the ID slot from the regressResult or interactionResult class
getID-method | Class to Contain the Regression Result Based on An Interaction Model
getID-method | Class to Contain the Regression Result
getIndex | Access the SignificantIndex slot from the regressResult or interactionResult class
getIndex-method | Class to Contain the Regression Result Based on An Interaction Model
getIndex-method | Class to Contain the Regression Result
getInteraction | Access the interaction slot from the contrastMatrix class
getInteraction-method | Class to Contain the Contrast Matrix that Used for Linear Regression
getIntIndex | Access the IntIndex slot from the designMatrix class
getIntIndex-method | Class to Contain the Design Matrix that Used for Linear Regression
getLength | Calculate the Length of interactionResult class
getLength-method | Class to Contain the Regression Result Based on An Interaction Model
getLevel | Access the level slot from the contrastMatrix class
getLevel-method | Class to Contain the Contrast Matrix that Used for Linear Regression
getNormalizationMethod | Access the significantIndex slot from the regressResult or interactionResult class
getNormalizationMethod-method | Class to Contain the Regression Result Based on An Interaction Model
getNormalizationMethod-method | Class to Contain the Regression Result
getP | Access the pValue slot from regressResult or interactionResult class
getP-method | Class to Contain the Regression Result Based on An Interaction Model
getP-method | Class to Contain the Regression Result
getPCutoff | Access the significantPvalueCutoff slot from regressResult or interactionResult class
getPCutoff-method | Class to Contain the Regression Result Based on An Interaction Model
getPCutoff-method | Class to Contain the Regression Result
getTarget | Access the target slots from the designMatrix class
getTarget-method | Class to Contain the Design Matrix that Used for Linear Regression

## -- H --

hugene10stCONTROL | hugene10stCONTROL

## -- I --

initialize-method | Class to Contain the Contrast Matrix that Used for Linear Regression
initialize-method | Class to Contain the Design Matrix that Used for Linear Regression
interactionResult | Class to Contain the Regression Result Based on An Interaction Model
interactionResult-class | Class to Contain the Regression Result Based on An Interaction Model

## -- M --

mogene10stCONTROL | mogene10stCONTROL

## -- O --

output.cls | Create *.CLS file for GSEA analysis
output.gct | Create an *.GCT file for GSEA analysis
output.ing | Create an Ingenuity File for Ingenuity Analysis
Output2HTML | Creating HTML file for regressResult or interactionResult class
Output2HTML-method | Class to Contain the Regression Result Based on An Interaction Model
Output2HTML-method | Class to Contain the Regression Result

## -- P --

pDataExample | a phenoData example
postInteraction | Create an Object of InteractionResult Class for Testing Interaction
preProcess3prime | A wrapper function to normalize the the 3 prime array
preProcessGeneST | Proprocess genechip ST array

## -- Q --

qa3prime | Creating Quality Assessment Report for 3 Prime Array
qaGeneST | Creating Quality Assessment Report for Gene ST Array
QC | sample QC result from Affy Expression Console

## -- R --

regress | Run regression to fit genewise linear model
regressionMethod | Access the regressionMethod slot from the regressResult or interactionResult class
regressionMethod-method | Class to Contain the Regression Result Based on An Interaction Model
regressionMethod-method | Class to Contain the Regression Result
regressResult | Class to Contain the Regression Result
regressResult-class | Class to Contain the Regression Result

## -- S --

selectSigGene | select differentially expressed genes from the regressResult class
selectSigGene-method | Class to Contain the Regression Result Based on An Interaction Model
selectSigGene-method | Class to Contain the Regression Result
selectSigGeneInt | select differentially expressed genes from the interactionResult class
show-method | Class to Contain the Contrast Matrix that Used for Linear Regression
show-method | Class to Contain the Design Matrix that Used for Linear Regression
show-method | Class to Contain the Regression Result Based on An Interaction Model
show-method | Class to Contain the Regression Result
Sort | Sort a regressionResult or an interactionResult
Sort-method | Class to Contain the Regression Result Based on An Interaction Model
Sort-method | Class to Contain the Regression Result
summary-method | Class to Contain the Regression Result Based on An Interaction Model
summary-method | Class to Contain the Regression Result