This script reads MS data and converts it to a convenient form for further analysis.
Other scripts may take advantage using:
from intensities import *
Note this also includes numpy as np, scipy as sp and pandas as pd.
Features:
- Read the proteinGroups.txt table into a PANDAS DataFrames
- Extract relative intensity matrices for the four sample classes (WCL, WCLp, UB, UBp)
- Log2-transform experiment : control relative intensity ratios (fold-change)
- Prepare DataFrames containing the fold-change values and indexed on protein name
Use intensities.py output to produce histograms of the MS data.
Use intensities.py output to compute proteins having sufficiently large positive or negative fold-change values in a particular experiment.
Use itensities.py output for global analysis of all experiments.
Currently:
- Compute principal components of WCL experiments
- Plot first 2 PCs' against each other