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

Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.

Yudong D He1, Hongyue Dai, Eric E Schadt

  • 1Rosetta Inpharmatics Inc., 12 040 115th Avenue Northeast, Kirkland, WA 98034, USA. yudong_he@merck.com

Bioinformatics (Oxford, England)
|May 23, 2003
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

Elective genomic sequencing for adults in research, clinical and commercial contexts.

medRxiv : the preprint server for health sciences·2026
Same author

A transcriptional program associated with neurotransmission in the living human brain.

Molecular psychiatry·2026
Same author

Establishing the relationship between brain cellular senescence and brain structure.

Cell·2026
Same author

Artificial Intelligence Monitoring of Neurological Status From Patient Videos in the Neuroscience Intensive Care Unit.

Neurosurgery·2026
Same author

A Collection of Patient-Derived Intestinal Organoid Lines Reveals Epithelial Phenotypes Associated with Genetic Drivers of Pediatric Inflammatory Bowel Disease.

Inflammatory bowel diseases·2025
Same author

Toward governance of artificial intelligence in pediatric healthcare.

NPJ digital medicine·2025
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

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

This study introduces a standardized framework for microarray analysis, offering a robust dataset and performance metrics. This aims to improve the comparison and development of analytical methods for gene expression profiling.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microarray expression profiling methods are rapidly advancing.
  • Lack of standardized comparison frameworks leads to confusion in selecting optimal analytical and experimental designs.
  • A need exists for objective criteria to evaluate and improve microarray data analysis.

Purpose of the Study:

  • To establish a standard framework for comparing and improving analytical and statistical methods in microarray data analysis.
  • To provide a comprehensive dataset and proposed figures of merit for performance assessment.
  • To facilitate objective choices between different microarray platforms, experiment designs, and data processing approaches.

Main Methods:

  • Developed a microarray dataset with 204 in-situ synthesized oligonucleotide arrays.

Related Experiment Videos

  • Utilized two-color cDNA samples from 20 diverse human tissues and cell lines.
  • Designed approximately 24,000 60-mer oligonucleotides targeting ~2500 known genes.
  • Designed hybridization experiments to support performance assessment of various data processing and experimental designs.

    • Main Results:

    • Generated a standardized dataset of 204 oligonucleotide arrays hybridized with human tissue/cell line samples.
    • Proposed standard figures of merit for evaluating differential expression detection and pattern similarity analysis.
    • The dataset and metrics are designed to support the assessment of image processing, normalization, error modeling, and other analytical methods.

    Conclusions:

    • The proposed dataset and figures of merit provide a crucial standard framework for the microarray community.
    • Facilitates objective comparison and improvement of diverse analytical and statistical methods for gene expression data.
    • Aims to reduce confusion and enhance the reliability of microarray expression profiling results.