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Classification of RNA-seq Data

  • Kean Ming Tan
  • Ashley Petersen
  • Daniela Witten
Chapter
Part of the Frontiers in Probability and the Statistical Sciences book series (FROPROSTAS)

Abstract

Next-generation sequencing technologies have made it possible to obtain, at a relatively low cost, a detailed snapshot of the RNA transcripts present in a tissue sample. The resulting reads are usually binned by gene, exon, or other region of interest; thus the data typically amount to read counts for tens of thousands of features, on no more than dozens or hundreds of observations. It is often of interest to use these data to develop a classifier in order to assign an observation to one of several pre-defined classes. However, the high dimensionality of the data poses statistical challenges: because there are far more features than observations, many existing classification techniques cannot be directly applied. In recent years, a number of proposals have been made to extend existing classification approaches to the high-dimensional setting. In this chapter, we discuss the use of, and modifications to, logistic regression, linear discriminant analysis, principal components analysis, partial least squares, and the support vector machine in the high-dimensional setting. We illustrate these methods on two RNA-sequencing data sets.

Keywords

Support Vector Machine Partial Little Square Linear Discriminant Analysis Support Vector Classifier Sparse Principal Component Analysis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

D.W. received support for this work from NIH Grant DP5OD009145, NSF CAREER Award DMS-1252624, and a Sloan Foundation Research Fellowship.

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Authors and Affiliations

  1. 1.Department of BiostatisticsUniversity of WashingtonSeattleUSA

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