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  1. IGB
  2. IGBF-4205

GAGE and Pathview on Kelsey Unpol data

        Details

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

          Description

          GOAL: To run GAGE on Kelsey's unpollinated pistil data.

          We have reached the need for further annotation of the results.
          Will try a first pass at geting the R code to work, and then pass it along to Brandon to try the various permutations of the experiment.

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              is blocked by

              Task - A task that needs to be done. IGBF-4210 Search for updated KEGG Ids for tomato

              • Major - Major loss of function.
              • Closed

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                robofjoy Robert Reid added a comment -

                Close this ticket out and make new ones as needed as we have all sorts of new things to troubleshoot.

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                robofjoy Robert Reid added a comment - Close this ticket out and make new ones as needed as we have all sorts of new things to troubleshoot.
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                robofjoy Robert Reid added a comment -

                Trying the updated table made by Brandon.
                Is here:
                https://drive.google.com/file/d/1o7yeWg2BDzlHPJHshyT3r5bi9LWjVVKp/view?usp=drive_link

                Table is now a TPM normalized.
                And had a column of RefSeq Ids and Kegg IDs.

                Show
                robofjoy Robert Reid added a comment - Trying the updated table made by Brandon. Is here: https://drive.google.com/file/d/1o7yeWg2BDzlHPJHshyT3r5bi9LWjVVKp/view?usp=drive_link Table is now a TPM normalized. And had a column of RefSeq Ids and Kegg IDs.
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                robofjoy Robert Reid added a comment -

                PathView runs great on the data.

                Gage however has been causing me fits. There is something about the table that gage does not like
                Tested code on a Sweet potato dataset and it all works great.

                Show
                robofjoy Robert Reid added a comment - PathView runs great on the data. Gage however has been causing me fits. There is something about the table that gage does not like Tested code on a Sweet potato dataset and it all works great.

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    Dates

                    • Created:
                      Updated:
                      Resolved: