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:1
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Sprint:Fall 4 2023 Oct 16, Fall 5
Description
File: FindTreatmentEffectAcrossGenotypes-DESeq2.Rmd
Check to see if the analysis and the interaction term is explained well and provides enough sanity checking to confirm no significance.
Use bar plot shiny app to show analysis.
During meeting with Muday Lab, we found a gene that we thought ought to have come up in a test of the interaction term: Solyc02g063355.1
The SL5 version of that gene appears in the top row of the attached heat map file 2023-10-19-meeting-heatmap-visualization.png.
The heat map shows log2(average(cpm(A.28/V.28))) for treatment durations indicated on the x axis of the plot.
Attachments
Activity
There should be 6 DE genes when the threshold for log2foldchange is 0. The code from the branch in this ticket should have a threshold of 0 and the 6 significant genes are only present at 30 minutes. The code is at the very top of the markdown that indicates the threshold. Do you see this occurrence? It is also stated in the knitted pdf how many DE genes are present at each time chunk. The 6 genes I found to be significant are the 6 genes in the barplots in the above comment. Thanks!
[~RobertReid]
Confirmed !!
I see the 6 genes below the P-adjusted cutoff at 30 minutes (SL4) once the LFC threshold is set to 0.
Are there any other pieces here that need review?
That is all that needs to be reviewed. Thank you!
Creating a PR!
Testing:
- Had no issues knitting the markdown.
- Results files are saved and organized properly.
- Comprehension & grammar are fine. Might need to improve further later on.
Moving to done!
Confirming the Analysis with bar plots of gene expression: