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:3
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Sprint:Fall 2 2023 Sep 17
Description
The time course data set includes genotypes are, VF36, F3H
For this task, create some code that tests the interaction between temperature and genotype.
Note: We will have results for every time point individually.
Goal: Find genes that respond differently to heat stress depending on genotype.
For example, is there a gene that increases expression in response to heat in the "are" genotype and decreases expression in response to heat in the "VF36" genotype?
Suggestions for how to do these things:
- Read section from DESeq2 manual description testing of interactions between variables: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions
- review design creation: https://youtu.be/X6p3E-QTcUc?t=646
- This was also helpful: https://hbctraining.github.io/DGE_workshop/lessons/04_DGE_DESeq2_analysis.html