Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:1
-
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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3446 [ 22548 ] |
| Summary | Improve information on interaction term in the markdown | Improve information on interaction term in markdown |
| 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. |
*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. |
| 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. |
*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 |
| Attachment | 2023-10-19-meeting-heatmap-visualization.png [ 18068 ] |
| 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 |
*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 Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Solyc09g092690.3-interaction-genotypeVStemp.png [ 18069 ] | |
| Attachment | Solyc04g011440.4-interaction-genotypeVStemp.png [ 18070 ] | |
| Attachment | Solyc06g076560.2-interaction-genotypeVStemp.png [ 18071 ] | |
| Attachment | Solyc01g102960.3-interaction-genotypeVStemp.png [ 18072 ] | |
| Attachment | Solyc03g117630.1-interaction-genotypeVStemp.png [ 18073 ] | |
| Attachment | Solyc03g120090.1-interaction-genotypeVStemp.png [ 18074 ] |
| 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 Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
*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 Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
| 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 Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
*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 * Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
| 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 * Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
*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 * Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
| 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 * Reviewed this gene in results excel files and it is present in the file but not as significant as some others which are references in a comment below. The Arabidopsis homolog of this gene appears to encode a gene with a very well-studied role in heat stress response. It binds to lipids and appears to be expressed in mature pollen, if I am reading this diagram correctly: https://www.arabidopsis.org/servlets/TairObject?name=AT1G48590 |
*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 numbers shown are log2(average(cpm(VF |
| 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 numbers shown are log2(average(cpm(VF |
*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. |
| Assignee | Molly Davis [ molly ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Robert Reid [ robertreid ] | Molly Davis [ molly ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Fall 4 2023 Oct 16 [ 180 ] | Fall 4 2023 Oct 16, Fall 5 [ 180, 181 ] |
| Rank | Ranked higher |
| Assignee | Molly Davis [ molly ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |