Exploring Gene Expression Data, Using Plots

Date
2007-01-01
Authors
Nikolau, Basil
Cook, Dianne
Hofmann, Heike
Lee, Eun-Kyung
Wurtele, Eve
Yang, Hao
Nikolau, Basil
Wurtele, Eve
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Research Projects
Organizational Units
Journal Issue
Series
Department
Biochemistry, Biophysics and Molecular BiologyStatisticsGenetics, Development and Cell Biology
Abstract

This paper describes how to explore gene expression data using a combination of graphical and numerical methods. We start from the general methodology for multivariate data visualization, describing heatmaps, parallel coordinate plots and scatterplots. We propose new methods for gene expression data analysis using direct manipulation graphics. With linked scatterplots and parallel coordinate plots we explore gene expression data differently than many common practices. To check replicates in relation to treatments we introduce a new type of plot called a “replicate line” plot. There is a worked example, that focuses on an experimental study containing two two-level factors, genotype and cofactor presence, with two replicates.

Comments

This article is from Journal of Data Science 5 (2007): 151. Posted with permission.

Description
Keywords
Citation
DOI
Source
Collections