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Analyzing Peptide Microarray Data with the R pepStat Package

, : Analyzing Peptide Microarray Data with the R pepStat Package. Methods in Molecular Biology 1352: 127-142

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.


PMID: 26490472

DOI: 10.1007/978-1-4939-3037-1_10

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