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yingshansambi / qbb2023-answers

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Week 9 Feedback #10

Open dtaylo95 opened 10 months ago

dtaylo95 commented 10 months ago

Regrade 12/14/2023

Python script to run DE analysis

5.75/6

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 1

Great work! I think your Jaccard index is a bit off but only because you're not actually filtering to significant genes in your homemade analysis. You ARE getting rid of genes whose p-val is nan, which is good, but the significant genes are the ones whose padj < 0.1. Because you're skipping this filtering step, you're essentially comparing the genes that are significant in the DESeq2 analysis to almost all of the genes from the homemade analysis (significant or not).

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: 9.75/10

Great work! Feel free to fix that minor issue and resubmit

yingshansambi commented 9 months ago

Hi Dylan, I have resubmitted my week 9 assignment. Sorry for submitting late! Thank you so much for checking!!

dtaylo95 commented 9 months ago

Regrade 12/14/2023

Great work! I updated the rubric above. Current grade: 9.75/10. Feel free to fix the minor issue and resubmit for the full 10/10.