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 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...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

You might also read

Related Articles

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

Sort by
Same author

Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End.

Genome research·2026
Same author

The E3-ome gene-centric compendium reveals the human E3 ligase landscape.

Cell·2026
Same author

A comprehensive evaluation of long-read de novo transcriptome assembly.

Genome biology·2026
Same author

<i>Alpseq</i>: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing.

mAbs·2026
Same author

stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data.

NAR genomics and bioinformatics·2025
Same author

Selecting differential splicing methods: Practical considerations for short-read RNA sequencing.

F1000Research·2025
Same journal

Detection, communication, and individual identification with deep audio embeddings: A case study with North Atlantic right whales.

PLoS computational biology·2026
Same journal

Exploring the structural lexicon of the Proteome via Metric Geometry.

PLoS computational biology·2026
Same journal

Linking retinal sampling in neural encoding models to temporal profiles of visual processing in humans.

PLoS computational biology·2026
Same journal

CAdir: Joint clustering of cells and genes for single-cell transcriptomics with visualization-driven cluster quality assessment.

PLoS computational biology·2026
Same journal

Systematic design of auxotrophic strains and media conditions to probe metabolic functions in E. coli.

PLoS computational biology·2026
Same journal

Neuronal excitability and parameter variability in the Hodgkin-Huxley model.

PLoS computational biology·2026
See all related articles

Related Experiment Video

Updated: May 26, 2026

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces
12:04

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Published on: March 1, 2017

BeadArray expression analysis using bioconductor.

Matthew E Ritchie1, Mark J Dunning, Mike L Smith

  • 1Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. mritchie@wehi.edu.au

Plos Computational Biology
|December 7, 2011
PubMed
Summary
This summary is machine-generated.

This study explores open-source Bioconductor tools for analyzing Illumina whole-genome expression BeadArray data. It demonstrates a complete workflow from data import to differential expression analysis.

More Related Videos

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Related Experiment Videos

Last Updated: May 26, 2026

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces
12:04

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Published on: March 1, 2017

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Illumina whole-genome expression BeadArrays are widely used for gene profiling.
  • Vendor-specific software (GenomeStudio/BeadStudio) is available, but open-source alternatives offer flexibility.

Purpose of the Study:

  • To explore and demonstrate the use of Bioconductor open-source software packages for analyzing Illumina BeadArray data.
  • To provide a comprehensive workflow for BeadArray data analysis, including differential expression assessment.

Main Methods:

  • Utilizing Bioconductor packages for data import and quality assessment.
  • Applying preprocessing and annotation techniques tailored for BeadArray data.
  • Demonstrating differential expression analysis in designed experiments.

Main Results:

  • Successful application of Bioconductor tools for a complete BeadArray data analysis pipeline.
  • Comprehensive coverage of essential steps from data handling to statistical analysis.

Conclusions:

  • Bioconductor offers a powerful and flexible open-source alternative for Illumina BeadArray data analysis.
  • The demonstrated workflow facilitates robust gene expression profiling and differential expression studies.