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  1. IGB
  2. IGBF-4244

Deseq2 Normalization summary

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        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          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.

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              robofjoy Robert Reid added a comment -

              This is done since Brandon found the feature in pathview. So this is done.

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              robofjoy Robert Reid added a comment - This is done since Brandon found the feature in pathview. So this is done.
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              robofjoy Robert Reid added a comment -

              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.

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              robofjoy Robert Reid added a comment - 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.

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                • Assignee:
                  robofjoy Robert Reid
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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