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Analyzing Peptide Microarray Data with the R pepStat Package

  • Gregory Imholte
  • Renan Sauteraud
  • Raphael Gottardo
Part of the Methods in Molecular Biology book series (MIMB, volume 1352)

Abstract

In this chapter we demonstrate the use of R Bioconductor packages pepStat and Pviz on a set of paired peptide microarrays generated from vaccine trial data. Data import, background correction, normalization, and summarization techniques are presented. We introduce a sliding mean method for amplifying signal and reducing noise in the data, and show the value of gathering paired samples from subjects. Useful visual summaries are presented, and we introduce a simple method for setting a decision rule for subject/peptide responses that can be used with a set of control peptides or placebo subjects.

Key words

Normalization False discovery rate Data visualization Baseline correction Decision rule Sliding mean Smoothing Background correction 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Gregory Imholte
    • 1
  • Renan Sauteraud
    • 1
  • Raphael Gottardo
    • 1
  1. 1.Vaccine and Infectious Disease DivisionFred Hutchinson Cancer Research CenterSeattleUSA

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