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  1. IGB
  2. IGBF-3281

Muday-144 DE analysis & Volcano Plots

        Details

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

          Combining Ticket IGBF-3279 with this ticket IGBF-3281:

          2. I know that pipelines/analysis procedures evolve. Can you look at the analysis of DE genes with temperature within each genotype and make sure we have a final set of data. This is pertinent to compare with number 3! I think we decided that IQR 50 was the best metric
          4. Volcano plots with lines drawn at p values (not adjusted p-values) less than 0.05 and Log fold change (base 2) of 1.0. This would be comparing temperature response within genotypes (so 3 plots) and differences between genotypes at each temperature (so 6 plots).

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              Task - A task that needs to be done. IGBF-3278 Muday-144 PCA Plots

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3279 Muday-144 Analysis of DE genes

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis added a comment -

                3-D Volcano Plots: https://cran.r-project.org/web/packages/volcano3D/vignettes/Vignette.html

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                Mdavis4290 Molly Davis added a comment - 3-D Volcano Plots: https://cran.r-project.org/web/packages/volcano3D/vignettes/Vignette.html
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                ann.loraine Ann Loraine added a comment -

                vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

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                ann.loraine Ann Loraine added a comment - vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
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                Mdavis4290 Molly Davis added a comment -

                Updated Bitbucket

                Repository: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/

                Commit: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/commits/67b6a52222e71dd5dfd4f721c82cf8b88ebd4769

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                Mdavis4290 Molly Davis added a comment - Updated Bitbucket Repository: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/src/main/ Commit: https://bitbucket.org/mdavis4290/analysis-flavonoid-rnaseq/commits/67b6a52222e71dd5dfd4f721c82cf8b88ebd4769
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                ann.loraine Ann Loraine added a comment -

                Merged changes into main branch of team repository and then added 3 new commits to address comments on above commit. Moving to Done.

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                ann.loraine Ann Loraine added a comment - Merged changes into main branch of team repository and then added 3 new commits to address comments on above commit. Moving to Done.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                    Dates

                    • Created:
                      Updated:
                      Resolved: