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Two-stage testing in microarray analysis: what is gained?
Journal article   Open access   Peer reviewed

Two-stage testing in microarray analysis: what is gained?

David B Allison and Christopher S Coffey
The journals of gerontology. Series A, Biological sciences and medical sciences, Vol.57(5), pp.B189-B192
05/2002
DOI: 10.1093/gerona/57.5.B189
PMID: 11983715
url
https://doi.org/10.1093/gerona/57.5.B189View
Published (Version of record) Open Access

Abstract

Microarray technology for gene expression studies offers powerful new technology for understanding changes in gene expression as a function of other observable or manipulable variables. However, microarrays also pose a number of new challenges. One of the most prominent of these is the difficulty in establishing a procedure for declaring whether a gene's expression level is associated with the independent variable that offers reasonable and specifiable false-positive (type 1 error) and false-negative (type 2 error) rates. A recent article described a two-stage testing procedure to address these goals. However, information was not provided to indicate whether this procedure would or would not meet its objectives. Herein, we show mathematically that the two-stage procedure proposed does not provide benefits in terms of minimizing false-negatives while controlling the false-positive rate relative to standard single-stage testing. Therefore, investigators are encouraged to consider alternative analytic approaches.
 Animals False Negative Reactions False Positive Reactions Male Mice Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - standards

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