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:4
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Epic Link:
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Sprint:Fall 1 - Sep 5, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21
Description
Talked with Gloria on Tuesday.
She is delighted with all that has been accomplished.
But to get to publication she needs 2 more pieces of the puzzles
- Analysis comparing genes expressed at different time points (within each plant variety)
- Analysis comparing genes expressed btw genotypes
She has requested we tackle this!!!
Anthony has defended and his finishing the details. But he will focus on publication soon after that is done.
Step 1 in this should be to set up a chat with Gloria and better define the scope of what this task should be!
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link |
|
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | SL4_SL5_Description.R [ 17922 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17923 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17923 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17924 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17924 ] |
| Attachment | SL4_SL5_Description.R [ 17922 ] |
| Attachment | SL4_SL5_Description.R [ 17925 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17926 ] |
| Summary | Time course Analysis between genotypes. And analysis comparing time points | Analyze Muday time points and genotypes |
| Sprint | Summer 6 2023 July 24 [ 175 ] |
| Attachment | SL4_SL5_counts_muday-144.csv [ 17927 ] |
| Summary | Analyze Muday time points and genotypes | Plan Muday time points and genotypes analysis |
| Sprint | Summer 6 2023 July 24 [ 175 ] | Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] | Molly Davis [ molly ] |
| Attachment | SL4_SL5_Description.R [ 17925 ] |
| Attachment | SL4_SL5_description_tomato.csv [ 17926 ] |
| Attachment | SL4_SL5_counts_muday-144.csv [ 17927 ] |
| Comment |
[ Dr. Muday also asked for the SL4 gene names to be their own column with the description. So I made an R script and created an output file with the columns "SL4, SL5, Description". I also just added the new SL4 column to the original counts file.
Script: [^SL4_SL5_Description.R] File with just gene names and description: [^SL4_SL5_description_tomato.csv] File with SL4 column added on to the end of original counts file: [^SL4_SL5_counts_muday-144.csv] ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Molly Davis [ molly ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 6 2023 July 24, Summer 7 2023 Aug 7 [ 175, 176 ] | Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 175, 176, 177 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 175, 176, 177 ] | Testing 2 : 4 Nov - 15 Nov, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21 [ 82, 175, 176, 177 ] |
| Rank | Ranked higher |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Molly Davis [ molly ] |
| Link | This issue relates to IGBF-3437 [ IGBF-3437 ] |
| Comment |
[ *EdgeR comment*:
I don't see much reason to switch to edgeR. I think it is best to stick to our analysis method to keep consistent results with the dataset. DESeq and EdgeR are very similar and both assume that no genes are differentially expressed. DESeq uses a "geometric" normalisation strategy, whereas EdgeR is a weighted mean of log ratios-based method. Both normalise data initially via the calculation of size / normalisation factors. So I think changing now would be unnecessary as I already have DESeq being used in volcano plots and pca plots that they want to publish. If we were to change analysis methods now we would have to redo previous plots. For example, we would want to compare volcano plots or previous results to the new ones so that would be more difficult switching and comparing DESeq results to EdgeR results. Overall, I think it would be best to stick to our DESeq method for now only because we want to stay consistent. But I understand wanting to see different plots possibly from EdgeR and we could see basic results from edgeR but for continuing the genotype and time analysis' it might be best to stick to DESeq probably. DESeq documentation I use: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html Let me know what you think! :) [~aloraine] ] |
| Link | This issue relates to IGBF-3438 [ IGBF-3438 ] |
| Link | This issue relates to IGBF-3439 [ IGBF-3439 ] |
| Link | This issue relates to IGBF-3440 [ IGBF-3440 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |