nasa / nasa/GeneLab_Data_Processing
[BulkRNASeq] Handle processing with experimental groups where N = 1
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Description
Description
Certain datasets have experimental groups of single samples.
This current breaks differential expression approaches and likely means differential expression will be impossible.
Steps to Reproduce
- Create subset of Runsheet rows with at least one group with N = 1 samples
Expected Behavior
Processing workflows should identify these cases and process up to DE but not run DE.
In these cases, normalized data should be available for release.
Actual Behavior
Processing attempts DE and raises exception.
Impact on Data
Non silent bug: no processed data released with this causing an issue.
Known to impact 1 dataset at start of this issue.
Additional Context
Provide any additional information or context that might be relevant to the issue.
Possible Solution (optional)
Process through normalization, then stop.
This will require some modification for post processing which assumes complete processing.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start from the BulkRNASeq processing workflow and locate where differential expression runs after normalization, then trace the post-processing assumptions that require complete processing. Done means datasets with an experimental group of N = 1 reach normalization, skip differential expression without an exception, and make normalized data available for release.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100