Evaluation of microarray data normalization procedures using spike-in experiments

Background: Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spikein experiments, it is possible to characterize the analyzed data and thereby enable comparisons of different analysis methods. Results: A spike-in experiment using eight in-house produced arrays was used to evaluate established and novel methods for filtration, background adjustment, scanning, channel adjustment, and censoring. The S-plus package EDMA, a stand-alone tool providing characterization of analyzed cDNA-microarray data obtained from spike-in experiments, was developed and used to evaluate 252 normalization methods. For all analyses, the sensitivities at low false positive rates were observed together with estimates of the overall bias and the standard deviation. In general, there was a trade-off between the ability of the analyses to identify differentially expressed genes (i.e. the analy...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Patrik Rydén, Henrik Andersson, Mattias Landfors, Linda Näslund, Blanka Hartmanová, Laila Noppa, Anders Sjöstedt
• Keywords: Analyses, Analysis, Analyzed Data, BMCBI 2006