This lesson is still being designed and assembled (Pre-Alpha version)

Research Data Management: Assignments

Description

Assignments are mainly designed for student curriculums but can be also used to test your working knowledge upon self-study.

Assignments

Each assigment comprises two comparisons (comp #1 and comp #2).

Assignment 1

seed infection dpi comparison assignment
MgCl2 P. syringae DC3000 2 comp #1 A1
S. melonis Fr1 P. syringae DC3000 2 comp #1 A1
MgCl2 P. syringae DC3000 7 comp #2 A1
S. melonis Fr1 P. syringae DC3000 7 comp #2 A1

Assignment 2

seed infection dpi comparison assignment
MgCl2 Mock 2 comp #1 A2
MgCl2 P. syringae DC3000 2 comp #1 A2
MgCl2 Mock 7 comp #2 A2
MgCl2 P. syringae DC3000 7 comp #2 A2

Assignment 3

seed infection dpi comparison assignment
M. extorquens PA1 Mock 2 comp #1 A3
S. melonis Fr1 Mock 2 comp #1 A3
M. extorquens PA1 Mock 7 comp #2 A3
S. melonis Fr1 Mock 7 comp #2 A3

Assigment 4

seed infection dpi comparison assignment
M. extorquens PA1 P. syringae DC3000 2 comp #1 A4
S. melonis Fr1 P. syringae DC3000 2 comp #1 A4
M. extorquens PA1 P. syringae DC3000 7 comp #2 A4
S. melonis Fr1 P. syringae DC3000 7 comp #2 A4

Tasks

  1. Rephrase the scientific question (0.5 point).
  2. Compute the tables of differential expressed genes for both comparisons. Create a histogram of corrected p-values for each comparison (QC). Annotate the genes with their gene symbols and annotation using biomartr (2 points).
  3. Create a volcano plot for each comparison to display the differential genes. Justify your choice for the fold change cutoff based on the distribution of your log2 fold change values (e.g. median, 75th percentile, etc).