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  1. IGB
  2. IGBF-3462

Even Expression failure in EBSEQ-HMM

        Details

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

          Description

          EBSEQ-HMM should be able to predict whether gene increase or decrease over time using a HMM.

          And it does this well!
          BUT it should also be able to identify when states go from "Even expression" to high or low.

          And I can't seem to detect any genes that do this.
          Example:

          "c..Up.Up.Up....14...Down.Up.Up....40...Up.Down.Up....169...Down.Down.Up....59.."
          "Up-Up-Up" 14
          "Down-Up-Up" 40
          "Up-Down-Up" 169
          "Down-Down-Up" 59
          "Up-Up-Down" 13
          "Down-Up-Down" 207
          "Up-Down-Down" 32
          "EE-Up-Up" 0
          "Up-EE-Up" 0
          "EE-EE-Up" 0
          "Down-EE-Up" 0
          "EE-Down-Up" 0
          "Up-Up-EE" 0
          "EE-Up-EE" 0
          "Down-Up-EE" 0
          "Up-EE-EE" 0
          "Up-Down-EE" 0
          "EE-Up-Down" 0
          "Up-EE-Down" 0
          "Down-Down-Down" 3
          "Down-EE-EE" 0
          "EE-Down-EE" 0
          "Down-Down-EE" 0
          "EE-EE-Down" 0
          "Down-EE-Down" 0
          "EE-Down-Down" 0

          EE means even expression.
          They are all zero.
          And that happens in all 6 instances. Which is EXTREMELY unlikley.
          I am missing something.
          So this task is to figure out what I am missing!

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3454 Develop an R prototype script EB-Seq using Muday time course

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                robofjoy Robert Reid created issue -
                robofjoy Robert Reid made changes -
                Field Original Value New Value
                Epic Link IGBF-3446 [ 22548 ]
                robofjoy Robert Reid made changes -
                Link This issue blocks IGBF-3454 [ IGBF-3454 ]
                robofjoy Robert Reid made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                I was wrong, it appears to have worked! There are not many however.

                An excerpt from the results.

                "Solyc12g089340.2" "Up-Down-Up"
                "Solyc12g094570.1" "Down-Down-Up"
                "Solyc12g094600.3" "Down-Up-Up"
                "Solyc12g094690.1" "EE-EE-Down"
                "Solyc12g094700.3" -

                Show
                robofjoy Robert Reid added a comment - I was wrong, it appears to have worked! There are not many however. An excerpt from the results. "Solyc12g089340.2" "Up-Down-Up" "Solyc12g094570.1" "Down-Down-Up" "Solyc12g094600.3" "Down-Up-Up" "Solyc12g094690.1" "EE-EE-Down" "Solyc12g094700.3" -
                robofjoy Robert Reid made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                I am marking this as done as it no longer appears to be an issue.

                Show
                robofjoy Robert Reid added a comment - I am marking this as done as it no longer appears to be an issue.

                  People

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

                    • Created:
                      Updated:
                      Resolved: