a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.

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Documentation for package ‘DEqMS’ version 1.0.1

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equalMedianNormalization normalize to have equal medians in all samples
farmsSummary summarize peptide/PSM intensity into protein level relative abundance by factor analysis
medianSummary summarize peptide/PSM intensity into protein level relative abundance estimate by taking the median
medianSweeping summarize peptide/PSM intensity into protein level relative abundance estimate by median sweeping method
medpolishSummary summarize peptide/PSM intensity into protein level relative abundance estimate by Turkey median polish procedure
outputResult output the DEqMS analysis results in a data frame
peptideProfilePlot plot log2 intensities of all peptides for one gene in different samples
plotFitCurve plot the fitted prior variance against the number of quantified peptides or PSMs
spectraCounteBayes Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression