AffyExpress (version 1.38.0)

Affymetrix Quality Assessment and Analysis Tool

Description

The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

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Version

1.38.0

License

LGPL

Maintainer

Arthur Li

Last Published

February 15th, 2017

Functions in AffyExpress (1.38.0)

AffyInteraction

Analyze interaction effect and produce output

result2html

output differentially expressed genes to a HTML file

Filter

filter an 'ExpressionSet' using different methods

interaction.result2html

output differentially expressed genes for the interaction model to a HTML file

AffyRegress

Select differentially expressed genes, and output the result to a html file

import.data

Importing Affy Cel File

pre.process

Data Preprocessing

regress

Run regression to fit genewise linear model

testData

AffyBatch instance testData

AffyQA

Microarray quality control and assessment

make.contrast

Create a contrast matrix

post.interaction

Create a list of tables for the result based on the main effect variable

make.design

Create a Design Matrix

select.sig.gene

select differentially expressed genes based on p value and/or fold change