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
That is all that needs to be reviewed. Thank you!
Creating a PR!
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?
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]
Confirming the Analysis with bar plots of gene expression:
- Changed log-fold change threshold to 0.5 and only got 1 DE gene at just 30 min. Changed to 0.1 and got 5 DE genes at just 30 min. Changed to 0.05 and still only got the exact same 5 DE genes at 30min from before. Change to 0 fold change threshold and got 6 DE genes at 30 min. These genes are:
- Solyc09g092690.3
- Solyc04g011440.4
- Solyc06g076560.2
- Solyc01g102960.3
- Solyc03g117630.1
- Solyc03g120090.1
- Reviewed the 6 DE genes at 30 min in the expression barplot Dr. Loraine made to confirm analysis (https://ann-loraine-gmail.shinyapps.io/72_F3H_PollenTube/) seen above. These genes meet the statistical design of being DE across genotype VF36 plus ARE and the temperatures 28C and 34C. In other words, we are answering the question: is the condition effect different across genotypes?
- Wrote in more detail of what was used and why in the markdown.
Testing:
Moving to done!