Week 9 Feedback

[dtaylo95]

Python script to run DE analysis

5.5/6

Exercise	Points Possible	Grade
Implementation of manual DE test	1	1
Manual DE test on all genes	1	1
Code to do FDR correction	1	1
Running PyDESeq2 on all genes	1	1
Overlap between methods	1	0.75
Code to produce volcano plot	1	0.75

I think the way you're calculating Jaccard index isn't quite right. We want to calculate n_genes_sig_in_both_analyses / n_genes_sig_in_either_analysis. It looks like you're calculating the numerator correctly (the intersection between the two gene sets): https://github.com/CucHuynh/qbb2023-answers/blob/b0cca7bda20c27635aa7e9a5033df7f88521319d/week9/week9HW.py#L87-L88 We want the denominator to be the union of the two gene sets. Currently you're calculating the denominator as the number of genes significant in the homemade analysis plus the number of genes significant in the deseq2 analysis, but this will double count any genes that are significant in both.

Your volcano plot looks great but we asked you to only highlight points with padj <0.1 (which you did) AND whose abs(log2FoldChange) > 1 (which you did not do).

README.md with answers to questions

1/1

Exercise	Points Possible	Grade
Jaccard index overlap between methods	1	1

Output text files

2/2

Exercise	Points Possible	Grade
List of DE genes in manual test	1	1
List of DE genes in PyDESeq2 test	1	1

Pretty plots

1/1

Exercise	Points Possible	Grade
Exercise 2 Volcano plot	1	1

Grade

Total: 9.5/10

Great work! Feel free to fix those two minor issues and resubmit!

[dtaylo95]

Regrade 12/15/2023

I updated the rubric above. Current grade: 9.5/10

Great work! Feel free to fix those two small things and resubmit for the full 10/10