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  1. IGB
  2. IGBF-4312

Use Deseq results to define Up-Down patterns in ManuSeq

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9, Spring 1, Spring 2, Spring 3

          Description

          GOAL: We tweak our UP-Down patterns so that we are actually using deseq's results to define whether a gene goes up or down.

          No longer using just the general pattern derived from the normalized data. We goo a few steps furhter in the Deseq script and get the results.

          I predict this will produce wayyyy less up and down patterns and way more even-even type of responses.

          We will need to compare the overall #'s of how many Up-down, up-up, etc we get this way compared to the "version 1" method. (manuseq)

          We will call this way version 2 until we come up with a cooler name. (Pattern de seq)

          Also need to refresh our brains on how Deseq2 defines its cutoffs for significance. We can play with that. We can be less stringent so we get more "ups and downs".

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              robofjoy Robert Reid created issue -
              robofjoy Robert Reid made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
              Sprint Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9, Spring 1 [ 225, 226, 227, 228, 229, 230, 231, 232, 233 ] Fall 2, Fall 3, Fall 4, Fall 5, Fall 6, Fall 7, Fall 8, Fall 9, Spring 1, Spring 2 [ 225, 226, 227, 228, 229, 230, 231, 232, 233, 234 ]
              ann.loraine Ann Loraine made changes -
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              robofjoy Robert Reid made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
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              ann.loraine Ann Loraine made changes -
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              bbendick Brandon Bendickson made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]

                People

                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                  Dates

                  • Created:
                    Updated: