# Affymetrix Quality Assessment and Analysis Tool

## Documentation for package ‘AffyExpress’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AffyInteraction | Analyze interaction effect and produce output
AffyQA | Microarray quality control and assessment
AffyRegress | Select differentially expressed genes, and output the result to a html file
Filter | filter an 'ExpressionSet' using different methods
import.data | Importing Affy Cel File
interaction.result2html | output differentially expressed genes for the interaction model to a HTML file
make.contrast | Create a contrast matrix
make.design | Create a Design Matrix
post.interaction | Create a list of tables for the result based on the main effect variable
pre.process | Data Preprocessing
regress | Run regression to fit genewise linear model
result2html | output differentially expressed genes to a HTML file
select.sig.gene | select differentially expressed genes based on p value and/or fold change
testData | AffyBatch instance testData