Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:4
-
Epic Link:
-
Sprint:Spring 4 2023 Feb 21, Spring 5 2023 Mar 6
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).
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Link | This issue blocks IGBF-3280 [ IGBF-3280 ] |
| Link | This issue is blocked by IGBF-3282 [ IGBF-3282 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Spring 4 2023 Feb 21 [ 164 ] | Spring 4 2023 Feb 21, Spring 5 2023 Mar 6 [ 164, 165 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Description | 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). |
Combining Ticket 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). |
| Summary | Muday-144 Volcano Plots | Muday-144 DE analysis & Volcano Plots |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Merged changes into main branch of team repository and then added 3 new commits to address comments on above commit. Moving to Done.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
3-D Volcano Plots: https://cran.r-project.org/web/packages/volcano3D/vignettes/Vignette.html