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  1. IGB
  2. IGBF-3448

Report edgeR and DESeq2 temperature-only DE genes from SL4 and SL5

        Details

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

          Description

          For this task:

          • Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
          • Do the same for SL4 annotations
          • Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
          • Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
          • Migrate volcano plot code to Common.R and show padj cutoff on the y axis
          • Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results

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              Task - A task that needs to be done. IGBF-3455 Visualize log fold-changes and p values to compare edgeR and DESeq2 results

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3446 [ 22548 ]
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 DE genes Compare edgeR to DESeq2 DE genes using SL4 and SL5 gene counts
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 DE genes using SL4 and SL5 gene counts Compare edgeR to DESeq2 temp-only DE genes using SL4 and SL5 gene counts
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 temp-only DE genes using SL4 and SL5 gene counts Compare edgeR to DESeq2 temp-only DE genes from SL4 and SL5
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotaiotns used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)
                ann.loraine Ann Loraine made changes -
                Summary Compare edgeR to DESeq2 temp-only DE genes from SL4 and SL5 Compare and sanity-check edgeR and DESeq2 temperature-only DE genes from SL4 and SL5
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 2 2023 Sep 17 [ 178 ] Fall 1 - Sep 5 [ 82 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 - Sep 5 [ 82 ] Fall 1 - Sep 5, Fall 2 2023 Sep 17 [ 82, 178 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and generalize it to use pvalue or adjusted pvalue (add new parameter with pvalue as the default)
                * Make a new Markdown that makes volcano plots for both edgeR and DESeq2 results and also for both SL4 and SL5 (do SL5 first)                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                * Visualize log fold-changes and p values to compare edgeR and DESeq2 results
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                Changes are now part of the main branch in the repository. Since I skipped over the review step, I'm moving the ticket forward to "needs testing" column.

                EdgeR and DESeq temperature effects testing are now in these files:

                • FindControlVsStressDEGenes-SL5-DESeq2.Rmd
                • FindControlVsStressDEGenes-SL5-edgeR.Rmd
                • FindControlVsStressDEGenes-SL4-DESeq2.Rmd
                • FindControlVsStressDEGenes-SL4-edgeR.Rmd

                Suggestion on how to test and/or review:

                • read the "pdf" files corresponding to each of the above Markdowns.
                • confirm that "txt" for SL4, SL5 analyzed with DESeq2 and edgeR all exist in the "results" subdirectory
                • confirm that .pdf files for the same genome version report the same "git hash" for the repository
                Show
                ann.loraine Ann Loraine added a comment - - edited Changes are now part of the main branch in the repository. Since I skipped over the review step, I'm moving the ticket forward to "needs testing" column. EdgeR and DESeq temperature effects testing are now in these files: FindControlVsStressDEGenes-SL5-DESeq2.Rmd FindControlVsStressDEGenes-SL5-edgeR.Rmd FindControlVsStressDEGenes-SL4-DESeq2.Rmd FindControlVsStressDEGenes-SL4-edgeR.Rmd Suggestion on how to test and/or review: read the "pdf" files corresponding to each of the above Markdowns. confirm that "txt" for SL4, SL5 analyzed with DESeq2 and edgeR all exist in the "results" subdirectory confirm that .pdf files for the same genome version report the same "git hash" for the repository
                ann.loraine Ann Loraine made changes -
                Description For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                * Visualize log fold-changes and p values to compare edgeR and DESeq2 results                 		For this task:

                * Complete Markdowns documenting / executing different temperature, same genotype and treatment duration DE analysis for SL5 annotations using edgeR and DESeq2
                * Do the same for SL4 annotations
                * Rename Markdowns (if necessary) to indicate both the method (edgeR or DESeq2) and the genome assembly annotations used (SL4 or SL5)
                * Make sure the data files written out for the SL5 analyses contain a column with SL4 gene names, if available
                * Migrate volcano plot code to Common.R and show padj cutoff on the y axis
                * Add volcano plots to edgeR and DESeq2 Markdowns to visualize DE results
                ann.loraine Ann Loraine made changes -
                Summary Compare and sanity-check edgeR and DESeq2 temperature-only DE genes from SL4 and SL5 Report edgeR and DESeq2 temperature-only DE genes from SL4 and SL5
                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 ]
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3455 [ IGBF-3455 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment -

                Testing:

                • FindControlVsStressDEGenes-SL4-DESeq2.pdf = Good
                • results/CvT-DESeq2-SL4.txt = Good
                • FindControlVsStressDEGenes-SL4-edgeR.pdf = Good
                • results/CvT-edgeR-SL4.txt = Good
                • FindControlVsStressDEGenes-SL5-DESeq2.pdf = Good
                • results/CvT-DESeq2-SL5.txt = Good
                • FindControlVsStressDEGenes-SL5-edgeR.pdf = Good
                • results/CvT-edgeR-SL5.txt = Good
                Show
                Mdavis4290 Molly Davis added a comment - Testing : FindControlVsStressDEGenes-SL4-DESeq2.pdf = Good results/CvT-DESeq2-SL4.txt = Good FindControlVsStressDEGenes-SL4-edgeR.pdf = Good results/CvT-edgeR-SL4.txt = Good FindControlVsStressDEGenes-SL5-DESeq2.pdf = Good results/CvT-DESeq2-SL5.txt = Good FindControlVsStressDEGenes-SL5-edgeR.pdf = Good results/CvT-edgeR-SL5.txt = Good
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    • Created:
                      Updated:
                      Resolved: