nasa / nasa/GeneLab_Data_Processing

[BulkRNASeq] Handle processing with experimental groups where N = 1

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Dominant language
Jupyter Notebook
Stars
125
Forks
65
PR merge metrics
No merged PRs in 30d

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

  1. 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

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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