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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:
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          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

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                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
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                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
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                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

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