Date on Master's Thesis/Doctoral Dissertation
12-2010
Document Type
Master's Thesis
Degree Name
M.S.
Department
Computer Engineering and Computer Science
Committee Chair
Rouchka, Eric Christian
Author's Keywords
MiRNA; Microarray; Normalization
Subject
Small interfering RNA
Abstract
Multiple normalization methods have been proposed for the analysis of microRNA microarray expression profiles but there is no consensus method. One of the more robust methods, quantile normalization, is commonly used in transcript (mRNA) studies and was therefore used for normalizing the first microRNA expression profiles of the NCI-60 cell panel, published in 2007. In this study the appropriateness of VSN-Inv, a recently proposed alternative normalization method, to the NCI-60 dataset is verified. VSN-Inv normalization results in much increased inter-sample correlations among control groups, and significantly higher intra-chip correlations of duplicate probes, versus quantile and no normalization. Furthermore, VSN-Inv normalization was found to have favorable performance for hierarchical clustering and discovery of miRNA-mRNA interactions, and a lower misclassification rate for predictive analysis based on tissue of origin when using log transformed data (median 0.19, best 0.12).
Recommended Citation
Disibio, Martin T., "Assessment and performance of VSN-INV normalization on the NCI-60 microRNA expression profiles." (2010). Electronic Theses and Dissertations. Paper 354.
https://doi.org/10.18297/etd/354
