AlexsLemonade / AlexsLemonade/refinebio

Dataset request GSE56080

Open
#2,275 7 comments 0 reactions 0 assignees View on GitHub
dataset request illumina beadchip
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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.