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Related Experiment Videos

Multiplicity issues in microarray experiments.

F Bretz1, J Landgrebe, E Brunner

  • 1B and SR, Novartis Pharma AG, Lichtstr. 35, 4002 Basel, Switzerland. frank.bretz@novartis.com

Methods of Information in Medicine
|August 23, 2005
PubMed
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For microarray experiments, familywise error rate (FWER) controlling procedures can be too conservative. False discovery rate (FDR) controlling methods offer a better balance for gene expression data analysis.

Area of Science:

  • Genomics
  • Bioinformatics
  • Statistical Genetics

Background:

  • Microarray experiments generate high-dimensional data, necessitating robust statistical methods for analysis.
  • Multiple testing procedures are crucial for controlling errors when analyzing large-scale genomic datasets.

Purpose of the Study:

  • To discuss error concepts relevant to microarray experiments.
  • To review and compare multiple testing procedures for gene expression data analysis.
  • To evaluate the suitability of familywise error rate (FWER) and false discovery rate (FDR) controlling methods.

Main Methods:

  • Focus on FWER and false discovery rate (FDR) controlling procedures.
  • Investigation of Bonferroni-type methods, modified Bonferroni, data-driven approaches, and linear step-up methods.

Related Experiment Videos

  • Detailed description of assumptions, advantages, and limitations of each method.

    • Main Results:

    • FWER controlling procedures are often overly conservative in high-dimensional screening.
    • FDR controlling procedures provide a better balance between raw and adjusted P-values.
    • FDR-based methods may be more appropriate for gene expression data analysis in certain contexts.

    Conclusions:

    • The choice of error concept and multiple testing procedure remains an open question for microarray analysis.
    • While FDR and its variants are promising, long-term validation for microarray data is still needed.
    • Further experience is required to fully assess the validity of multiple testing procedures in this field.