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**Wrangler responsible for this dataset/lab:**
Primary: Ami
Secondary: Enrique
**Description of the task:**
GSE116222: EpithelialDiversityHealthInflammation
https://docs.google.com/spre…
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**Describe the bug**
Running the hca_to_scea script produces the following error:
`script.py: error: the following arguments are required: -study`
even though the -study argument is included.
**To …
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Whenever we trigger the GEO importer for bulk RNA-seq experiments, the freshly converted MAGE-TAB file (with name E-GEOD-xxx.idf.txt) gets copied to the $ATLAS_PROD/GEO_import/GEOD/E-GEOD-xxx/ folder …
anjaf updated
3 years ago
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Hi,
I'm not sure I'm doing this correctly but I recently encountered the SDRF for PXD010154, which contains files from a "Q Exactive Plus" instrument. But the instrument ontology code was MS:1002526,…
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My data comes from [here](https://ftp.pride.ebi.ac.uk/pride/data/proteomes/proteogenomics/differential-expression/RPMID25238572.2-organism-part/proteomics_lfq/out_msstats.csv).
When I run the dataPro…
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I am running the UPS data set with the --add_decoy option:
```
nextflow run nf-core/proteomicslfq -r 1.0.0 -profile docker --input https://raw.githubusercontent.com/bigbio/proteomics-metadata-standa…
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@daichengxin:
The following sdrf https://github.com/multiomics/multiomics-configs/blob/master/datasets/absolute-expression/tissues/PXD004242/PXD004242-Sample-1.tsv when is converted to OpenMS expe…
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Issue: Experiments page has been broken for the experiment: E-MTAB-7316
[E-MTAB-7316](http://ves-hx-77:8080/gxa/sc/experiments/E-MTAB-7316) - 400 error.
User ticket on RT: https://helpdesk.ebi…
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When running the tool on a spreadsheet that was wrangled from a contributor rather than by the `geo-to-hca` script, there were a few assumptions that didn't hold and resulted in some mis-assignments i…
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@daichengxin :
Can you add to each SDRF in my fork https://github.com/ypriverol/proteomics-metadata-standard the field
`Technology Type` with the value: `proteomic profiling by mass spectr…