Today I went through my R script for the RobertsLab/project-pacific.oyster-larvae project. I have a Volcano Plot and a Comparison Plot. I also did some data process plots: Profile Plots and QC Plots. I am working on updating the MS Stats protocol, and will include all the resources I used to create those plots. Additionally, I am beginning to read through the Oyster-Larval-Proteomics-2015 paper and am working on finding some new relevant citations. My goal for the month is to finish this project and paper!
MS Stats protocol and plots
GitHub Issue #516
R Script: Skyline-to-MSstats-format-and-plots.R
Work-in-progress MSStats protocol: 03-MSStats-protocol.md
Resources used to create R Script:
- MS Stats R Package Manual
- MS Stats Manual
- Yaamini’s R Script
- Help from Meena Choi regarding my needing to add a column labeled “Fraction” with all cells containing “1”
Plots:
Goals for this week regarding this project:
- Understand what plots are and figure out what’s important
- Figure out if other plots should be made (to be created next week)
- Figure out if other analyses should be done (to be performed next week)
- Work on organizing all the information