batcheffectsdataset

Containing R codes that can be used to regenerate the figures for the manuscript:

DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects

mainfiles

mainfigures.Rmd: to regenerate the main figures in the manuscript (excluding figures in the usage notes)
usagenotes.Rmd: to regenerate the case study figures in the usage notes section

datafile

protein_matrix_DDA_A549_K562.csv: protein matrix csv for A549/K562 cell line DDA-PASEF dataset
protein_matrix_DIA_A549_K562.csv: protein matrix csv for A549/K562 cell line diaPASEF dataset
metadata_DDA_A549_K562.csv: metadata for A549/K562 datasets (class and batch factors of samples)
sampleannotation_DDA_A549_K562.csv: metadata for A549/K562 datasets, formatted for "ProBatch" package based plots

protein_matrix_DDA_HCC1806_HS578T.csv: protein matrix csv for HCC1806/HS578T cell line DDA-PASEF dataset
protein_matrix_DIA_HCC1806_HS578T.csv: protein matrix csv for HCC1806/HS578T cell line diaPASEF dataset
metadata_DDA_HCC1806_HS578T.csv: metadata forHCC1806/HS578T datasets (class and batch factors for samples)
sampleannotation_DDA_HCC1806_HS578T.csv: metadata for HCC1806/HS578T datasets, formatted for "ProBatch" package based plots