Bioinformatics strategies for cDNA-microarray data processing
2009 (English)In: Batch effects and noise in microarray experiments: sources and solutions / [ed] Scherer, Andreas, Wiley and Sons , 2009, 1, , 272 p.61-74 p.Chapter in book (Other academic)
Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper pre-processing it is likely that the biological conclusions will be misleading. However, there are many alternatives and in order to choose a proper pre-processing procedure it is necessary to understand the effect of different methods. This chapter discusses several pre-processing steps, including image analysis, background correction, normalization, and filtering. Spike-in data are used to illustrate how different procedures affect the analytical ability to detect differentially expressed genes and estimate their regulation. The result shows that pre-processing has a major impact on both the experiment’s sensitivity andits bias. However, general recommendations are hard to give, since pre-processing consists of several actions that are highly dependent on each other. Furthermore, it is likely that pre-processing have a major impact on downstream analysis, such as clustering and classification, and pre-processing methods should be developed and evaluated with this in mind.
Place, publisher, year, edition, pages
Wiley and Sons , 2009, 1. , 272 p.61-74 p.
, Wiley series in probability and statistics
Research subject Mathematical Statistics
IdentifiersURN: urn:nbn:se:umu:diva-30827ISBN: 978-0-470-74138-2OAI: oai:DiVA.org:umu-30827DiVA: diva2:287318