AlexsLemonade / AlexsLemonade/refinebio

Detect Affymetrix HGU133A-HGU133B "pairs" in an expression data-driven manner (automatically)

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backlog exploration SCIENCE! (A.K.A. research question)
Dominant language
Python
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135
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PR merge metrics
No merged PRs in 30d

Description

### New Issue Checklist
- [x] The title is short and descriptive
- [x] The issue contains an:
- [x] Idea (new feature, user story, etc)
- [ ] Problem
- [x] You have explained the:
- [x] Context
- [x] Problem or idea
- [x] Solution or next step

### Context

_Explain the conditions that led you to write this issue. If you are proposing a new feature, the context should be your user story. If this relates to a certain page or API endpoint, provide a link._

Older Affymetrix chips -- `hgu133a` and `hgu133b` -- sampled a smaller number of probes/genes. Sometimes samples would be run on both `hgu133a` and `hgu133b` to get better coverage of the transcriptome (sort of equivalent to running a sample using the later `hgu133plus2` platform) resulting in paired `a` and `b` samples.

### Problem or idea

_The context should lead to something, an idea or a problem that you’re facing._

It would be great to automatically detected these paired samples and combine the information from both chips. Prior to taking this approach, there will be a considerable number of missing values in these samples as compared to their genome-wide successors. Some kind of imputation approach may be the path forward. If we use a neural network-based approach to reconstruct the other "half" of the sample, we may find that the true paired sample is most highly correlated with our reconstructed values.

### Solution or next step

_You can tag others or simply leave it for further investigation, but you must propose a next step towards solving the issue._

It's fine to run SCAN on these samples as planned. We should investigate this further after we have processed a sufficient number of samples to design experiments for investigating this issue.

Here's an example experiment from ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-11908/

Contributor guide

No contributing guide indexed for this repository

Research direction

No files, tests, or code entry points are identified in the issue. Start by reviewing the existing SCAN processing and the ArrayExpress E-GEOD-11908 example, then define experiments for detecting paired hgu133a and hgu133b samples and evaluating imputation; the work is done when an agreed automatic approach is validated on processed data.

Written by the indexing model from the issue text.

Assessment

Tech stack
machine-learning, python
Domain
bioinformatics
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

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