Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Libaffy: software for processing Affymetrix GeneChip data.

Steven A Eschrich1, Andrew M Hoerter

  • 1H. Lee Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, FL 33612, USA. Steven.Eschrich@moffitt.org

Bioinformatics (Oxford, England)
|April 28, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Personalized treatment in HPV+ oropharynx cancer using genomic adjusted radiation dose.

The Journal of clinical investigation·2025
Same author

A Formative Evaluation of Interventions to Enhance Clinical Trial Diversity Guided by the Socioecological Model.

Cancers·2025
Same author

In Reply to Li.

International journal of radiation oncology, biology, physics·2025
Same author

Creation and Characterization of a Breast Cancer Tissue Microarray Including Black and White Patients from Florida and Hispanic Patients from Puerto Rico and Florida.

Cancer research communications·2025
Same author

Evaluating the Radiation Sensitivity Index and 12-Chemokine Gene Expression Signature for Clinical Use in a CLIA Laboratory.

Cancer research communications·2025
Same author

spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis.

Cancer research·2024
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

A new software library, libaffy, supports Affymetrix GeneChip microarrays and includes popular algorithms like MAS5.0 and RMA. It offers a modular design for pipelines and a graphical interface for users, enhancing gene expression analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Affymetrix GeneChip microarrays are widely adopted for gene expression studies.
  • The increasing volume of gene expression data necessitates efficient analysis tools.

Purpose of the Study:

  • To develop a software library supporting Affymetrix file formats.
  • To implement popular gene expression data summarization algorithms.
  • To provide a user-friendly graphical interface for data analysis.

Main Methods:

  • Development of a modular software library (libaffy).
  • Implementation of Microarray Analysis Suite 5.0 (MAS5.0) and Robust Multi-array Analysis (RMA) algorithms.
  • Creation of a graphical user interface (GENE).

Related Experiment Videos

Main Results:

  • The libaffy library successfully supports Affymetrix file formats.
  • MAS5.0 and RMA algorithms are implemented within the library.
  • A functional graphical interface (GENE) is available for end-users.

Conclusions:

  • libaffy provides a versatile and accessible tool for Affymetrix GeneChip data analysis.
  • The modular design facilitates integration into existing bioinformatics pipelines.
  • The software is freely available under the GNU GPL license.