AlexsLemonade / AlexsLemonade/refinebio

Dataset request GSE31704

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#2,274 2 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 [GSE31704](https://www.refine.bio/experiments/GSE31704).

### Problem or idea

[GSE31704](https://www.refine.bio/experiments/GSE31704) is an Illumina HumanHT-12 V4.0 expression beadchip experiment with 6 samples - none of which appear to be downloadable from refine.bio.

Copying an error message from the debug information from [GSM786857](https://www.refine.bio/samples/GSM786857)

```

Encountered error in R code while running illumina.R pipeline during processing of /home/user/data_store/processor_job_1319230/GSE31704_non-normalized.txt.sanitized: Command '['/usr/bin/Rscript', '--vanilla', '/home/user/data_refinery_workers/processors/illumina.R', '--probeId', 'ID_REF', '--expression', '8,6,12,10,2,4,2,4,6,8,10,12', '--detection', 'Detection Pval', '--platform', 'illuminaHumanv4', '--inputFile', '/home/user/data_store/processor_job_1319230/GSE31704_non-normalized.txt.sanitized', '--outputFile', '/home/user/data_store/processor_job_1319230/GSE31704_non-normalized.PCL', '--cores', '64']' returned non-zero exit status 1
```

The following jumps out at me:

```
'--expression', '8,6,12,10,2,4,2,4,6,8,10,12',
```

Which means we are specifying the column indices for columns that contain expression values twice.

This might have to do with the headers in [`GSE31704_non-normalized.txt`](ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE31nnn/GSE31704/suppl/GSE31704_non-normalized.txt.gz) - here's an excerpt:

| `ID_REF` | `IMR90 control-A.AVG_Signal` | `IMR90 control-A.Detection Pval` | `IMR90 control-B.AVG_Signal` | `IMR90 control-B.Detection Pval` |
|---|---|---|---|---|

### Solution or next step

1. Is it due to the specific headers in this file or is something else causing the error?
2. Is this a case that we should be able to handle or would it harm our ability to process BeadChip data overall?
3. Reprocess + notify _or_ notify the user that we will not be able to handle this case.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by inspecting the headers in GSE31704_non-normalized.txt and the illumina.R invocation shown in the report, focusing on the duplicated expression column indices. Reproduce the failure if possible and determine whether this header pattern is the cause. Done means deciding whether BeadChip data can be supported safely, then either reprocessing and notifying the user or documenting that this dataset cannot be handled.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
bioinformatics
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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