Spearman's footrule as a measure of cDNA microarray reproducibility

Genomics
Byung Soo KimHyun Cheol Chung

Abstract

Replication is a crucial aspect of microarray experiments, due to various sources of errors that persist even after systematic effects are removed. It has been confirmed that replication in microarray studies is not equivalent to duplication, and hence it is not a waste of scientific resources. Replication and reproducibility are the most important issues for microarray application in genomics. However, little attention has been paid to the assessment of reproducibility among replicates. Here we develop, using Spearman's footrule, a new measure of the reproducibility of cDNA microarrays, which is based on how consistently a gene's relative rank is maintained in two replicates. The reproducibility measure, termed index.R, has an R2-type operational interpretation. Index.R assesses reproducibility at the initial stage of the microarray data analysis even before normalization is done. We first define three layers of replicates, biological, technical, and hybridizational, which refer to different biological units, different mRNAs from the same tissue, and separate cDNAs from a cDNA pool. As the replicate layer moves down to a lower level, the experiment has fewer sources of errors and thus is expected to be more reproducible. To va...Continue Reading

Citations

Dec 25, 2009·Plant Physiology·Hubert RehrauerLars Hennig
Jun 28, 2007·Omics : a Journal of Integrative Biology·Tobias K Karakach, Peter D Wentzell
Dec 21, 2007·Insect Molecular Biology·L C BartholomayB M Christensen
Jun 15, 2016·BMC Research Notes·Hyejin Cho, Hui-Hsien Chou

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