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cat-e-r / qbb2023-answers

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Week 9 Feedback #10

Open dtaylo95 opened 12 months ago

dtaylo95 commented 12 months ago

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

It looks like the way you're calculating the Jaccard index isn't quite right. You're calculating sig_in_homemade_only / sig_in_both. What we want to be calculating is sig_in_both / sig_in_either. You've used .intersection() correctly to get the number of genes significantly DE in both analyses, I would recommend .union() to find the number of genes significantly DE in either analysis.

We were also expecting you to define DESeq2 significant genes based only on the padj and leave the log2FC cutoff for the volcano plot, but I'm not going to take off points for that.

Also for your volcano plot (and actually also your Jaccard index, the way you're doing it), it looks like you're setting your log2FC cutoff as genes whose abs(log2FC) is less than 1. We want genes whose abs(log2FC) is greater than 1, because these are the genes with the biggest differences between sexes.

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 address the two minor issues and resubmit!

dtaylo95 commented 11 months ago

Graded 12/08/23

Feel free to address the two minor issues and resubmit!