Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples

Di Wu; Michael P Gantier

doi:10.1007/7651_2015_239

Normalization of Affymetrix miRNA Microarrays for the Analysis of Cancer Samples

Methods Mol Biol. 2016:1375:1-10. doi: 10.1007/7651_2015_239.

Authors

Di Wu^{1

2}, Michael P Gantier^{3

4}

Affiliations

¹ Department of Statistics, Harvard University, Cambridge, MA, USA.
² Centre for Cancer Research, MIMR-PHI Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia.
³ Centre for Cancer Research, MIMR-PHI Institute of Medical Research, 27-31 Wright Street, Clayton, VIC, 3168, Australia. [email protected].
⁴ Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia. [email protected].

PMID: 25971910
DOI: 10.1007/7651_2015_239

Abstract

microRNA (miRNA) microarray normalization is a critical step for the identification of truly differentially expressed miRNAs. This is particularly important when dealing with cancer samples that have a global miRNA decrease. In this chapter, we provide a simple step-by-step procedure that can be used to normalize Affymetrix miRNA microarrays, relying on robust normal-exponential background correction with cyclic loess normalization.

Keywords: Affymetrix; Cancer samples; Normalization; miRNA microarray; microRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Computational Biology / standards
Genomics / methods*
Genomics / standards
Humans
MicroRNAs / genetics*
Neoplasms / diagnosis
Neoplasms / genetics*
Oligonucleotide Array Sequence Analysis / methods*
Oligonucleotide Array Sequence Analysis / standards
Reagent Kits, Diagnostic* / standards
Software

Substances

MicroRNAs
Reagent Kits, Diagnostic