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

## Documentation for package ‘DEqMS’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
Residualplot | plot the residuals against the number of quantified peptides/PSMs.
spectraCounteBayes | Peptide/Spectra Count Based Empirical Bayes Statistics for Differential Expression
VarianceBoxplot | generate a boxplot of the variance
VarianceScatterplot | generate a scatter plot of the variance