Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-212

Make Affymetrix probe set visualization available as a data set option

    Details

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

      Description

      *Link to User Support Conversation in JIRA:
      http://204.84.7.129/browse/IGBF-210

      A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

      This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

      Follow the steps below:

      1) Go to Affymetrix website and get files:
      -Probe Set Consensus Sequences
      -actual Probe Sets
      *(Make sure it is for the correct probe, they have similar names)

      2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

      3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
      "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

      4) Find a file with extension "Link.psl" for the genome version that the user is using.
      -Verify that it is the correct file for the specific genome.

      5) Open the "Link.psl" file in IGB.
      -Read Probe Set Documentation and Understand the Visualization".

      6) Contact Ann (and user possibly) about proceeding steps.

        Attachments

          Issue Links

            Activity

            mason Mason Meyer (Inactive) created issue -
            mason Mason Meyer (Inactive) made changes -
            Field Original Value New Value
            Description A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.
            A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            mason Mason Meyer (Inactive) made changes -
            Sprint Sprint 4 [ 9 ]
            Story Points 2
            mason Mason Meyer (Inactive) made changes -
            Assignee David Norris [ dcnorris ] Mason Meyer [ mason ]
            mason Mason Meyer (Inactive) made changes -
            Status Open [ 1 ] In Progress [ 3 ]
            mason Mason Meyer (Inactive) made changes -
            Description A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            mason Mason Meyer (Inactive) made changes -
            Status In Progress [ 3 ] Testing In Progress [ 10003 ]
            dcnorris David Norris (Inactive) made changes -
            Sprint Sprint 4 [ 9 ] Sprint 4, Sprint 5 [ 9, 10 ]
            dcnorris David Norris (Inactive) made changes -
            Rank Ranked higher
            dcnorris David Norris (Inactive) made changes -
            Rank Ranked lower
            mason Mason Meyer (Inactive) made changes -
            Description A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            *Link to User Support Issue in JIRA:
            http://204.84.7.129/browse/IGBF-210

            A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            mason Mason Meyer (Inactive) made changes -
            Description *Link to User Support Issue in JIRA:
            http://204.84.7.129/browse/IGBF-210

            A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            *Link to User Support Conversation in JIRA:
            http://204.84.7.129/browse/IGBF-210

            A user has communicated a need to visualize probe set information within IGB, however, Affymetrix is no longer supporting access to probe set information in IGB.

            This story was created to serve as a reminder to get the probe and design sequence information from Affymetrix so that we can make the probe set visualization available as a data set option in IGB.

            Follow the steps below:

            1) Go to Affymetrix website and get files:
                       -Probe Set Consensus Sequences
                       -actual Probe Sets
                        *(Make sure it is for the correct probe, they have similar names)

            2) Put files from step 1 in a place where Ann can get them (Dropbox, etc.) and add a link to this location in this JIRA issue.

            3) When probe sets are found, write to the user (Alex Tonks <TonksA@cardiff.ac.uk>) and tell him something like:
                          "We are currently working on this issue for you and have found some files but wanted to verify that these are the correct ones. They are arrays (ENTER ARRAY ID). Are these the correct ones? I also need to locate another file but need to know the exact human genome version that you are using (hg18, hg38?). Please let me know whenever you have time and I will continue to work towards a solution to your problem."

            4) Find a file with extension "Link.psl" for the genome version that the user is using.
                       -Verify that it is the correct file for the specific genome.

            5) Open the "Link.psl" file in IGB.
                       -Read Probe Set Documentation and Understand the Visualization".

            6) Contact Ann (and user possibly) about proceeding steps.
            mason Mason Meyer (Inactive) made changes -
            Status Testing In Progress [ 10003 ] Closed [ 6 ]
            Resolution Fixed [ 1 ]
            mason Mason Meyer (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            mason Mason Meyer (Inactive) made changes -
            Status Reopened [ 4 ] Closed [ 6 ]
            Resolution Done [ 10000 ]
            mason Mason Meyer (Inactive) made changes -
            Status Closed [ 6 ] Testing In Progress [ 10003 ]
            mason Mason Meyer (Inactive) made changes -
            Status Testing In Progress [ 10003 ] Closed [ 6 ]
            ann.loraine Ann Loraine made changes -
            Epic Link IGBF-236 [ 15233 ]
            mason Mason Meyer (Inactive) made changes -
            Link This issue relates to HELP-68 [ HELP-68 ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 15124 ] Fall 2019 Workflow Update [ 19227 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 19227 ] Revised Fall 2019 Workflow Update [ 21344 ]

              People

              • Assignee:
                mason Mason Meyer (Inactive)
                Reporter:
                mason Mason Meyer (Inactive)
              • Votes:
                0 Vote for this issue
                Watchers:
                1 Start watching this issue

                Dates

                • Created:
                  Updated:
                  Resolved: