This notebook will explain what pre-processing was done to the data, which includes:
The script
make_CCLE_comparable_matrix.py
combines all PTM data types (phosphorylation, methylation, acetylation) into a single tsv file. Then it averages duplicate measurements of cell lines (some cell lines were measured in two different plexes). Finally, it saves a tsv file with only the 37 cell lines that were found in the CCLE data.
The final combined PTM data with comparable cell lines is saved in
lung_cellline_3_1_16/lung_cl_all_ptm/all_ptm_ratios_CCLE_cl.tsv