workflow.md

AgLDI Data Analysis Workflow

Pre-Processing:

• Recalibration with flex Batch Processing using Internal_Silver_recalibration.FAMSMethod (realignment with silver ion adducts and cholesterol+Ag signal)

Export Parameters:

• imzML:
  • m/z 100 – 1000
  • No background removal, yes binning at 20,000 points
  • Export raw spectra from disk
• XML:
  • Rename all by their code names and trial (PA-1a, PA-2a, PA-3a)
  • Export all in one flexImaging file together (because S/N is fairly similar across)

Data Processing:

• Using the function IMSPeakStats3
  • Read all data
  • Split data by sampleROIs
    • Note: SampleROIs function only works with Cardinal v1, so you have to load R 3.4.4 (latest version) in order for this to work.
  • TIC normalization
  • Remove spectra with SN < 10
  • Calculate stats (ANOVA, Tukey) after removing top and bottom 10%
  • Export data into csv for further analysis