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

Objective method of comparing DNA microarray image analysis systems.

Edward L Korn1, Jens K Habermann, Madhvi B Upender

  • 1Biometric Research Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. korne@ctep.nci.nih.gov

Biotechniques
|June 24, 2004
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

Phase II Study of Adavosertib in Patients With Tumors Containing BRCA1 and BRCA2 Mutations: Results From the NCI-MATCH ECOG-ACRIN Cancer Research Group (EAY131) Subprotocol Z1I.

JCO precision oncology·2026
Same author

A comprehensive European Colorectal Cancer Cohort dataset.

Scientific data·2026
Same author

Larotrectinib in Patients With Tumors With <i>NTRK</i> Fusions: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol EAY131-Z1E.

JCO precision oncology·2026
Same author

Changing standard of care during a randomized trial: examples, considerations and guidelines.

Journal of the National Cancer Institute·2026
Same author

Crizotinib in Patients with Tumors with MET Amplification or Exon 14 Deletion: Results from the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocols C1 and C2.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same author

Phase II Study of Dabrafenib and Trametinib in Patients With Tumors With <i>BRAF</i><sup><i>V600E</i></sup> Mutations: Updated Results From NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol H.

JCO precision oncology·2026
Same journal

Investigating the interactomic landscape of survival motor neuron (SMN) and the SMNΔ7 truncated protein.

BioTechniques·2026
Same journal

Antigen retrieval-immunofluorescence on free floating sections to visualize the liver lobule and its cellular makeup.

BioTechniques·2026
Same journal

Special approach of droplet digital polymerase chain reaction (ddPCR) for transgene stability of a Chinese hamster ovary (CHO) cell line.

BioTechniques·2026
Same journal

Strand-specific quantification of L1 ORF0 and related transcripts by multiplex reverse transcription with tagged primers.

BioTechniques·2026
Same journal

Why and when should we choose digital PCR?

BioTechniques·2026
Same journal

Quantitative and unbiased lung alveolar septum assessment in an LPS experimental mouse model using 2D-spatial correlation image analysis from hematoxylin and eosin slides.

BioTechniques·2026
See all related articles

Comparing DNA microarray image analysis systems is crucial for accurate gene expression data. This study presents a systematic method using replicate experiments to objectively evaluate different image processing systems, demonstrating it with UCSF Spot and GenePix.

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Computational Biology

Background:

  • Numerous image analysis systems exist for processing laser-scanned DNA microarray images.
  • These systems convert pixel intensity data into gene expression or copy number summaries.
  • Existing systems vary in algorithms, usability, and cost, necessitating objective comparison methods.

Purpose of the Study:

  • To establish a systematic and objective method for comparing the performance of different DNA microarray image analysis systems.
  • To provide a standardized approach for evaluating the accuracy and reliability of gene expression data derived from various image processing tools.

Main Methods:

  • Development of a systematic methodology for comparing image processing results.
  • Utilization of a series of replicate microarray experiments to generate comparable data.

Related Experiment Videos

  • Application of the developed method to compare the UCSF Spot and GenePix image processing systems using cDNA microarray data.

    • Main Results:

    • Demonstrated a reproducible method for assessing the differences in output from various image analysis systems.
    • Provided a comparative analysis of cDNA microarray data processed by UCSF Spot and GenePix.
    • Highlighted the importance of objective evaluation for selecting appropriate image analysis tools.

    Conclusions:

    • The proposed systematic method offers an objective means to compare DNA microarray image analysis systems.
    • Objective comparison is essential for ensuring the reliability and reproducibility of gene expression analyses.
    • This approach facilitates informed decisions in selecting the most suitable image processing software for specific research needs.