Document Type

Article

Publication Date

2-27-2018

Identifier

DOI: 10.1371/journal.pone.0191758; PMCID: PMC5828440

Abstract

Quality control, global biases, normalization, and analysis methods for RNA-Seq data are quite different than those for microarray-based studies. The assumption of normality is reasonable for microarray based gene expression data; however, RNA-Seq data tend to follow an over-dispersed Poisson or negative binomial distribution. Little research has been done to assess how data transformations impact Gaussian model-based clustering with respect to clustering performance and accuracy in estimating the correct number of clusters in RNA-Seq data. In this article, we investigate Gaussian model-based clustering performance and accuracy in estimating the correct number of clusters by applying four data transformations (i.e., naïve, logarithmic, Blom, and variance stabilizing transformation) to simulated RNA-Seq data. To do so, an extensive simulation study was carried out in which the scenarios varied in terms of: how genes were selected to be included in the clustering analyses, size of the clusters, and number of clusters. Following the application of the different transformations to the simulated data, Gaussian model-based clustering was carried out. To assess clustering performance for each of the data transformations, the adjusted rand index, clustering error rate, and concordance index were utilized. As expected, our results showed that clustering performance was gained in scenarios where data transformations were applied to make the data appear "more" Gaussian in distribution.

Journal Title

PLoS One

Volume

13

Issue

2

MeSH Keywords

Cluster Analysis; Female; Humans; Likelihood Functions; Models, Genetic; Ovarian Neoplasms; Sequence Analysis, RNA

Keywords

Cluster Analysis; Female; Humans; Likelihood Functions; Models, Genetic; Ovarian Neoplasms; Sequence Analysis, RNA

Comments

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Publisher's Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0191758

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