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ArrayTools (version 1.32.0)

geneChip Analysis Package

Description

This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

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Version

Version

1.32.0

License

LGPL (>= 2.0)

Maintainer

Arthur Li

Last Published

February 15th, 2017

Functions in ArrayTools (1.32.0)

Access the multiple comparison adjustment method from the regressResult or interactionResult class

Creating an HTML index file

access the ID slot from the regressResult or interactionResult class

interactionResult-class

Class to Contain the Regression Result Based on An Interaction Model

access the annotation slot from the regressResult or interactionResult slot

Access the SignificantIndex slot from the regressResult or interactionResult class

postInteraction

Create an Object of InteractionResult Class for Testing Interaction

An ExpressionSet example

getNormalizationMethod

Access the significantIndex slot from the regressResult or interactionResult class

hugene10stCONTROL

hugene10stCONTROL

access the adjPVal slot from regressResult or interactionResult class

regressionMethod

Access the regressionMethod slot from the regressResult or interactionResult class

Access the level slot from the contrastMatrix class

Creating HTML file for regressResult or interactionResult class

filter an ExpressionSet using different methods

Access the significantPvalueCutoff slot from regressResult or interactionResult class

Create an Ingenuity File for Ingenuity Analysis

Access the compare2 slot from the contrastMatrix class

Accessing the covariates from the designMatrix class

createExpressionSet

Creating an ExpressionSet

regressResult-class

Class to Contain the Regression Result

Access the significantFCCutoff slot from the regressResult or interactionResult class

preProcessGeneST

Proprocess genechip ST array

select differentially expressed genes from the regressResult class

access the foldChange slot from regressionResult or interactionResult class

Sort a regressionResult or an interactionResult

a data.frame contains expression data

Class to Contain the Contrast Matrix that Used for Linear Regression

Access the design matrix from the designMatrix class

getFilterMethod

Access the filterMethod slot from the regressResult or interactionResult class

selectSigGeneInt

select differentially expressed genes from the interactionResult class

Run regression to fit genewise linear model

Class to Contain the Design Matrix that Used for Linear Regression

Calculate the Length of interactionResult class

a phenoData example

Access the Compare1 slot from the contrastMatrix

Access the foldChange slot from the regressResult or interactionResult class

mogene10stCONTROL

mogene10stCONTROL

Access the pValue slot from regressResult or interactionResult class

Creating Quality Assessment Report for Gene ST Array

Creating Quality Assessment Report for 3 Prime Array

createGSEAFiles

A Wrapper Function to create *.GCT and *.CLS for GSEA analysis

sample QC result from Affy Expression Console

createIngenuityFile

A Wrapper Function to Create Files for Ingenuity Analysis

Access the contrast matrix from the contrastMatrix class

Access the IntIndex slot from the designMatrix class

Access the interaction slot from the contrastMatrix class

Access the target slots from the designMatrix class

Create an *.GCT file for GSEA analysis

preProcess3prime

A wrapper function to normalize the the 3 prime array

Create *.CLS file for GSEA analysis