de_msempire: MS-EmpiRe implementation, a wrapper function for...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

MS-EmpiRe implementation, a wrapper function for msEmpiRe::de.ana()

Description

ref; PMID:31235637 ref; https://github.com/zimmerlab/MS-EmpiRe

Usage

de_msempire(eset, model_matrix, model_matrix_result_prop)

Arguments

eset	a Biobase ExpressionSet that contains the peptide log2 intensities
model_matrix	a stats::model.matrix() result that is supplied to limma::lmFit()
model_matrix_result_prop	the column name in model_matrix that should be returned as the resulting coefficient estimated by eBayes(). In MS-DAP workflows this is typically "condition"

Details

note; MS-EmpiRe crashes when all proteins have the same number of peptides (eg; filtering topn=1 or topn=3 and minpep=3)

TODO: proper standarderror computation

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.