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affy--analysis of Affymetrix GeneChip data at the probe level
Laurent Gautier1, Leslie Cope, Benjamin M Bolstad
1Center for Biological Sequence Analysis (CBS), Technical University of Denmark, Building 208, 2800 Lyngby, Denmark. laurent@cbs.dtu.dk
Bioinformatics (Oxford, England)
|February 13, 2004
Summary
The affy R package offers flexible tools for analyzing Affymetrix GeneChip data. It enables detailed probe-level analysis, crucial for accurate results from oligonucleotide arrays.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Affymetrix GeneChip data processing is a key area for data analysts.
- Several alternative methods to the original Affymetrix data processing procedure have been developed and adopted.
Purpose of the Study:
- To introduce the affy R package for Affymetrix GeneChip data analysis.
- To demonstrate the package's flexibility and capabilities in accessing and manipulating probe intensity data.
- To highlight the significance of probe-level analysis for the Affymetrix platform.
Main Methods:
- Utilizing the R programming language and the affy package.
- Implementing functions and classes within the affy package for data processing.
- Performing probe-level data analysis on Affymetrix GeneChip data.
Main Results:
- The affy package provides a robust framework for analyzing oligonucleotide array data.
- The package allows users to access and manipulate probe intensity data with high flexibility.
- Demonstrated the utility of probe-level analysis for Affymetrix GeneChip data.
Conclusions:
- The affy package is a valuable tool for researchers analyzing Affymetrix GeneChip data.
- Effective probe-level analysis is essential for reliable results from Affymetrix platforms.
- The package enhances the flexibility and control available to users in bioinformatics analyses.