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  1. IGB
  2. IGBF-3356

Revise edgeR differential expression code to output results tables

        Details

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

          Description

          The current version does not write out DE gene results. Also, the name of the file is not specific enough.

          For this task:

          • Change name of FindDifferentiallyExpressedGenes.Rmd (and its knitted .PDF) to: FindControlVsStressDEGenes-edgeR.Rmd
          • Write out a consolidated .txt file reporting differential expression results

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3342 Create scaled counts file for Muday analysis

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3355 Create Markdown consolidating DESeq treatment vs control analysis

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3277 [ 22158 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3355 [ IGBF-3355 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
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                ann.loraine Ann Loraine added a comment - - edited

                I pushed my changes to the main branch in the team repository. Sorry - this means you have to rebase your branch onto main.

                To test:

                • Proof-read knitted .PDF and point out text that does not make sense or formatting that looks weird or bad
                • Read .Rmd file and check for possible bugs or unnecessary statements and code
                • Check for literal values that should instead be reported via in-line R code
                • Attempt to knit the .Rmd file and make note of any errors
                • Open the new output file in RStudio and visually inspect it - look for numbers that seem nonsensical
                Show
                ann.loraine Ann Loraine added a comment - - edited I pushed my changes to the main branch in the team repository. Sorry - this means you have to rebase your branch onto main. To test: Proof-read knitted .PDF and point out text that does not make sense or formatting that looks weird or bad Read .Rmd file and check for possible bugs or unnecessary statements and code Check for literal values that should instead be reported via in-line R code Attempt to knit the .Rmd file and make note of any errors Open the new output file in RStudio and visually inspect it - look for numbers that seem nonsensical
                ann.loraine Ann Loraine made changes -
                Description The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and knitted .PDF) to:
                ann.loraine Ann Loraine made changes -
                Description The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and knitted .PDF) to:                 		The current version does not write out DE gene results. Also, the name of the file is not specific enough.

                For this task:

                * Change name of FindDifferentiallyExpressedGenes.Rmd (and its knitted .PDF) to: FindControlVsStressDEGenes-edgeR.Rmd
                * Write out a consolidated .txt file reporting differential expression results
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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                Mdavis4290 Molly Davis added a comment - - edited

                Testing:

                • Proof-read knitted .PDF: Looks professional and easy to comprehend. The new section for writing results also looks good
                • Read .Rmd file: Everything ran on my machine flawlessly and no issues. Everything matches up well with the knitted pdf file as well.
                • Check in-line R code: I don't see any bugs for the in-line coding.
                • Attempt to knit .Rmd file: I had no issues knitting the .Rmd file myself on my machine.
                • Open the new output file: The CvT.txt file did save to the results folder and does open as an excel file but could look a little cleaner based off of my machine. For example, I see no column names so you don't know what the numbers are from.
                Show
                Mdavis4290 Molly Davis added a comment - - edited Testing : Proof-read knitted .PDF : Looks professional and easy to comprehend. The new section for writing results also looks good Read .Rmd file : Everything ran on my machine flawlessly and no issues. Everything matches up well with the knitted pdf file as well. Check in-line R code : I don't see any bugs for the in-line coding. Attempt to knit .Rmd file : I had no issues knitting the .Rmd file myself on my machine. Open the new output file : The CvT.txt file did save to the results folder and does open as an excel file but could look a little cleaner based off of my machine. For example, I see no column names so you don't know what the numbers are from.
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Summer 2 2023 May 29 [ 171 ] Summer 2 2023 May 29, Summer 3 2023 June 12 [ 171, 172 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3342 [ IGBF-3342 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Thank you [~molly] for noticing the error in the results file.
                I have re-pushed a new version.

                Note that I also changed the name to include "edgeR" in the file name.
                The results file is now named "CvT-edgeR.txt".

                Show
                ann.loraine Ann Loraine added a comment - Thank you [~molly] for noticing the error in the results file. I have re-pushed a new version. Note that I also changed the name to include "edgeR" in the file name. The results file is now named "CvT-edgeR.txt".
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
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                Mdavis4290 Molly Davis added a comment -

                After reviewing all of the commits made to the main repo and viewing the output file "CvT-edgeR.txt", it seems everything is in order now and looks great! Moving to done!

                Show
                Mdavis4290 Molly Davis added a comment - After reviewing all of the commits made to the main repo and viewing the output file "CvT-edgeR.txt", it seems everything is in order now and looks great! Moving to done!
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ] Ann Loraine [ aloraine ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: