AlexsLemonade / AlexsLemonade/refinebio
Dataset request GSE56080
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
A user requested [GSE56080](https://www.refine.bio/experiments/GSE56080).
### Problem or idea
[GSE56080](https://www.refine.bio/experiments/GSE56080) is a Illumina MouseRef-8 v2.0 expression beadchip experiment with 4 samples - none of which are available from refine.bio currently.
This was last tried in December 2018. Here's one of the errors in the debug information for [GSM1354762](https://www.refine.bio/samples/GSM1354762):
```
Encountered error in R code while running illumina.R pipeline during processing of /home/user/data_store/processor_job_1622876/GSE56080_non-normalized.txt.sanitized: Command '['/usr/bin/Rscript', '--vanilla', '/home/user/data_refinery_workers/processors/illumina.R', '--probeId', 'ID_REF', '--expression', '2,6,10,14', '--detection', 'Detection Pval', '--platform', 'illuminaMousev2', '--inputFile', '/home/user/data_store/processor_job_1622876/GSE56080_non-normalized.txt.sanitized', '--outputFile', '/home/user/data_store/processor_job_1622876/GSE56080_non-normalized.PCL', '--cores', '64']' returned non-zero exit status -9
```
I have less of an idea of what's going on here compared to #2274 - maybe `returned non-zero exit status -9` + December 2018 will be a hint!
### Solution or next step
First question that comes to mind for me is: given this information, is it likely that rerunning will just work ™️ ?
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with the illumina.R pipeline and the recorded command for GSM1354762, then inspect the GSE56080 processing context and the December 2018 failure. Determine whether the exit status -9 is still reproducible and whether rerunning can make all four samples available from refine.bio.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics, data-engineering
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100