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 Video

Updated: May 11, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
09:27

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org.

Lars M T Eijssen1, Magali Jaillard, Michiel E Adriaens

  • 1Department of Bioinformatics-BiGCaT, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands. l.eijssen@maastrichtuniversity.nl

Nucleic Acids Research
|April 27, 2013
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

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

Sort by
Same author

Neural peer pressure: intercellular dynamics and emergent phenotypes in the mosaic Rett syndrome brain.

Cell communication and signaling : CCS·2026
Same author

Multi-omics characterization of developing forebrain organoids unravels the dynamic molecular events of Rett syndrome pathogenesis.

Journal of neurodevelopmental disorders·2026
Same author

Basic Science and Pathogenesis.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2025
Same author

Molecular pathways of kidney development and their applications to clinical research.

Kidney international·2025
Same author

Integrative analysis of 115 transcriptomic studies decodes the molecular landscape of neurodevelopmental disorders.

Communications biology·2025
Same author

The inconclusive superiority debate of allogeneic versus autologous MSCs in treating patients with HFrEF: a systematic review and meta-analysis of RCTs.

Stem cell research & therapy·2025
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

This study introduces a new, free tool for quality control (QC) and pre-processing of Affymetrix gene expression data. The tool simplifies complex genomics data analysis for researchers of all experience levels, improving data quality and reuse.

Area of Science:

  • Genomics
  • Bioinformatics
  • Data Science

Background:

  • Quality control (QC) is essential for reliable scientific data, particularly in genomics.
  • Genomics generates large datasets using complex technologies, posing QC challenges.
  • Existing QC and pre-processing methods for Affymetrix gene expression chips are often fragmented and difficult to use.

Purpose of the Study:

  • To develop an integrated, user-friendly tool for QC and pre-processing of Affymetrix gene expression data.
  • To address the lack of accessible tools for researchers with varying levels of experience in genomics data analysis.
  • To harmonize and extend existing Bioconductor functionalities for Affymetrix data.

Main Methods:

  • Developed a freely available tool integrating and extending Bioconductor packages.

More Related Videos

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

Related Experiment Videos

Last Updated: May 11, 2026

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
09:27

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

  • Implemented the tool through a web portal (http://www.arrayanalysis.org) with a wizard-like interface.
  • Provided extensive documentation, including user guides and interpretation aids.

    • Main Results:

    • The tool offers a unified solution for QC and pre-processing of Affymetrix gene expression data.
    • The web portal and downloadable R package cater to users of all experience levels.
    • Extensive documentation facilitates understanding and application of state-of-the-art methods.

    Conclusions:

    • The developed tool enhances data quality and promotes data reuse in genomics research.
    • Increased accessibility of advanced QC and pre-processing methods will foster adoption of standards.
    • This initiative supports the scientific community by simplifying complex genomics data analysis.