Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Summer 1, Summer 2
Description
GOAL:
Explore once again how Deseq2 does its normalization.
Are there any red flags as to why we cannot use this instead of RPKM, TPM etc.???
Capture in a Google slide deck in the Kelsey unpol folder.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 1 [ 218 ] | Summer 1, Summer 2 [ 218, 219 ] |
| Rank | Ranked higher |
This is done since Brandon found the feature in pathview. So this is done.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
https://docs.google.com/presentation/d/1E56wOOJ1xJgwJzF6pT_qXDcIUkFzC5JYvBDphF-wUYQ/edit?usp=sharing
This is a slide deck that summarizes what DEseq2 does when normalizing and gives explanations why not to use RPKM, etc.