Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.5
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Sprint:Fall 4 2023 Oct 16
Description
Make a new Markdown that compares genotypes are and VF36 within temperature, within treatment duration (time point), using same testing framework as C versus T comparisons.
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Activity
Thanks for the head's up [~molly]
I ended up making a new version of an existing Markdown, departing from my original plan, but I forgot to make a comment to that effect.
Files to review are already merged into main, and include:
- 72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.Rmd
- 72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.pdf
- 72_F3H_PollenTube/results/MvW-SL4.txt
- 72_F3H_PollenTube/results/MvW-SL5.txt
- 72_F3H_PollenTube/results/README.md
Review suggestions:
- check 72_F3H_PollenTube/results/MvW-SL4.txt for typos, nonsensical statements, formatting weirdnesses; check that there is a description of the data file output columns and what they mean
- try to read data files into R (keeping in mind that there are no possible row names due to no unique values per row, there is a header row, and column delimiter is a tab character)
- double-check that the sign of the fold-change is correct; log2 fold-change is supposed to be negative if are genotype is less than vf36 genotype; need to check the output of the linear model from first part of the file (A.28 and V.28) and the simpler two-group testing that was done in the later part of the file
- Confirm that the files related to this Markdown are well-documented in 72_F3H_PollenTube/results/README.md
- Observe that an older output of the file is missing (MvW-something...please see changes from commits, I removed two files)
Also see comment after this one with email sent to Muday lab and others summarizing the new content.
Note we should probably write an additional Markdown that makes volcano plots for an overview visualization of results. This could be an additional ticket.
Comments added advising on files to review and suggestions for review tasks.
cc: [~molly]
Notified Muday Lab and others with this email:
An update:
As per discussion on Friday and earlier in the week, I re-ran the comparisons between are and VF36 genotypes.
The new (revised) results files:
- 72_F3H_PollenTube/results/MvW-SL4.txt
- 72_F3H_PollenTube/results/MvW-SL5.txt
The R Markdown report from the code that made them:
- 72_F3H_PollenTube/FindMutantVsWildtypeDEGenes-DESeq2.pdf
The two results files contain comparisons between are and VF36, for 8 pairwise comparisons, comparing are and VF36 at 28 degrees or at 34 degrees, at each time point, individually. See columns "group1" and "group2" in a given row to see which six samples were compared to each other to produce the reported result.
I also included results from groups "A.28" and "V.28". These results came from testing for differences between genotypes, across all the time points, at 28 degrees. This finds the genes that are higher or lower in are, regardless of sample age or stage. You didn't ask for this specifically, but it gives a potentially useful portrait of expression differences between VF35 and are.
Also, I included every result obtained, not just the ones that exceeded thresholds.
Review:
- Output files are good
- Read the data files into R with no issues
- Sign of fold change is correct
- Output files are well documented in the markdown
- Previous output files were removed with this commit (https://bitbucket.org/hotpollen/flavonoid-rnaseq/commits/4d8fc79a8be7e7038d09d7a56de532a68b29db70)
Notes: From my understanding 8 pairwise comparisons were performed and combined on the results files. The comparison can be identified with the groups columns in the results output files. Might need to review this results file with Muday lab so they understand how to parse through output file and find the data they want to observe.
Thanks! [~aloraine]
Moving to done!
Need some more details of what to review and where please.