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You're reading from  R Bioinformatics Cookbook - Second Edition

Product typeBook
Published inOct 2023
PublisherPackt
ISBN-139781837634279
Edition2nd Edition
Concepts
Bioinformatics
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Author (1)
Dan MacLean
Dan MacLean
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Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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Estimating differential expression with DESeq2

The DEseq2 package is a popular tool for performing differential analysis of count data, so it is ideal for expression analysis of RNA-Seq data in R and other count data such as ChIPSeq.

DEseq2 performs normalization using a method called variance stabilizing transformation (VST), which is a type of transformation that aims to stabilize the variance of the data across the range of counts. This is in contrast to other normalization methods that aim to bring the mean of the data to a specific value, such as the mean of all the samples or the median of all the samples. The VST method is effective at reducing the variance of the data estimating with and improving the statistical power of differential expression analyses. This allows us to focus on improving gene ranking in results tables.

DEseq2 uses a negative binomial model to fit the count data and estimate the dispersion parameter. This model is commonly used for RNA-Seq data because...

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R Bioinformatics Cookbook - Second Edition
Published in: Oct 2023Publisher: PacktISBN-13: 9781837634279
© 2023 Packt Publishing Limited All Rights Reserved

Author (1)

author image
Dan MacLean

Professor Dan MacLean has a PhD in molecular biology from the University of Cambridge and gained postdoctoral experience in genomics and bioinformatics at Stanford University in California. Dan is now an honorary professor at the School of Computing Sciences at the University of East Anglia. He has worked in bioinformatics and plant pathogenomics, specializing in R and Bioconductor, and has developed analytical workflows in bioinformatics, genomics, genetics, image analysis, and proteomics at the Sainsbury Laboratory since 2006. Dan has developed and published software packages in R, Ruby, and Python, with over 100,000 downloads combined.
Read more about Dan MacLean

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