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

Adjustments and measures of differential expression for microarray data.

A Tsodikov1, A Szabo, D Jones

  • 1Huntsman Cancer Institute and Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112-5550, USA. alexander.tsodikov@hci.utah.edu

Bioinformatics (Oxford, England)
|February 16, 2002
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

Role of predelivery fetal echocardiography, cardiac magnetic resonance imaging and acute maternal hyperoxygenation in predicting urgency of neonatal balloon atrial septostomy in fetal dextro-transposition of the great arteries.

Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology·2026
Same author

Rate of prenatal diagnosis of critical congenital heart disease continued to improve despite COVID-19 pandemic: multicenter Canadian study.

Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology·2025
Same author

Hippocampal recording with a soft microelectrode array in a cranial window imaging scheme: a validation study.

Scientific reports·2024
Same author

Solitary humpback whales manufacture bubble-nets as tools to increase prey intake.

Royal Society open science·2024
Same author

Presentation of Meibomian Acini Compared to Dermal Papillae of the Eyelid Margin, Using Confocal Laser Scanning Microscopy and Corresponding Histology.

Klinische Monatsblatter fur Augenheilkunde·2024
Same author

Safety and feasibility pilot study of continuous low-dose maternal supplemental oxygen in fetal single ventricle heart disease.

Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology·2024

This study clarifies microarray data normalization, proposing a two-step method. Robust categorical adjustments proved superior to stochastic models for analyzing gene expression data.

Area of Science:

  • Bioinformatics
  • Statistical genomics
  • Computational biology

Background:

  • Microarray data analysis frequently employs complex, poorly understood normalization techniques.
  • Common methods normalize intensity ratios to a shared mean across genes.
  • Investigating the underlying statistical models and performance of these procedures is crucial.

Purpose of the Study:

  • To elucidate the statistical underpinnings of microarray data normalization procedures.
  • To compare the performance of various normalization and differential expression analysis methods.
  • To rank these methods for different microarray experiment types.

Main Methods:

  • A two-step statistical approach involving data transformation (slide-specific adjustment) was developed.

Related Experiment Videos

  • Statistical tests were applied to the transformed data for differential expression analysis.
  • Simulations and real colon cancer cell line data were used for comparison.

    • Main Results:

    • Robust categorical adjustments demonstrated superior performance compared to methods relying on precise stochastic models.
    • Some widely adopted normalization procedures were outperformed by robust categorical adjustments.
    • The proposed two-step procedure provides a framework for evaluating normalization techniques.

    Conclusions:

    • Robust categorical adjustments offer a more effective approach for analyzing microarray data than traditional stochastic models.
    • The study provides a benchmark for selecting appropriate normalization strategies in gene expression studies.
    • This research contributes to more reliable and accurate interpretation of microarray experimental results.