Web supplement to: “The effect of replication on gene expression microarray experiments”

Supplement to The effect of replication on gene expression microarray experiments.
Pavlidis P, Li Q, Noble WS pubmed reprint

Abstract

We examine the effect of replication on the detection of apparently differentially expressed genes in gene expression microarray experiments. Our analysis is based on a random sampling approach using real data sets from 16 published studies. We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication.

While dependent on the data source, our findings suggest that stable results are typically not obtained until at least five biological replicates have been used, and power is typically low. Conversely, for most studies, 10-15 replicates yield results that are quite stable, and there is less improvement in stability as the number of replicates is further increased. Our methods will be of use in evaluating existing data sets and in helping to design new studies.

Contact

paul@chibi.ubc.ca

Old Supplement Link

http://chibi.ubc.ca/gxrep/

Supplement

This web page contains additional data and descriptive material for our study on how changing the number of replicates affects the outcome of gene expression microarray experiments. The main areas are:

 

  • Data: Additional information on microarray data sources and how we used them.
  • Results: Additional results that supplement those shown in the paper.
  • Figures: Larger versions of the figures in the paper.