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  1. IGB
  2. IGBF-4243

Path view of various normalized tables

        Details

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

          Something is wrong with our tpm counts, I think it is the gene lengths. Lets try making some pathview images of our deseq normalized counts and even try normalizing the counts the way they do it in the Gage documentation. Ideally this would solve our issues.

          documentation: https://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/RNA-seqWorkflow.pdf

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              bbendick Brandon Bendickson created issue -
              bbendick Brandon Bendickson made changes -
              Field Original Value New Value
              Epic Link IGBF-2993 [ 21429 ]
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              bbendick Brandon Bendickson added a comment -

              Lets just keep using deseq normalized tables

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              bbendick Brandon Bendickson added a comment - Lets just keep using deseq normalized tables
              bbendick Brandon Bendickson made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Sprint Summer 2 [ 219 ] Summer 2, Summer 3 [ 219, 220 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ghouck Gabby Houck (Inactive) made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              ghouck Gabby Houck (Inactive) made changes -
              Status To-Do [ 10305 ] Pull Request Submitted [ 10101 ]
              ghouck Gabby Houck (Inactive) made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ghouck Gabby Houck (Inactive) made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ghouck Gabby Houck (Inactive) made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              ghouck Gabby Houck (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                People

                • Assignee:
                  ghouck Gabby Houck (Inactive)
                  Reporter:
                  bbendick Brandon Bendickson
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                  Dates

                  • Created:
                    Updated:
                    Resolved: