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waldronlab / curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataCuration/
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Control sample mislabeled as CRC in YuJ_2015 dataset #64

Closed CraigGin closed 2 years ago

CraigGin commented 2 years ago

Describe the bug I have been working with your CRC datasets and noticed that there are 75 samples with the study_condition labeled as "CRC" and 53 samples labeled as "control" in the YuJ_2015 dataset. This is in contrast to the published article which claims 74 CRC patients and 54 controls in their C1 cohort. By cross-referencing with other data sources, I was able to identify that the sample in question is the one with subject_id SZAXPI003427-1 and NCBI_accession ERR1018203. In both the European Nucleotide Archive and the NCBI database, this sample is labeled as "case", which agrees with your labeling. However, I checked with the first author of the paper, and the author was able to confirm that it should be labeled as a control. It would be great if this can be changed.

schifferl commented 2 years ago

Hi @CraigGin, I've transferred your issue to curatedMetagenomicDataCuration and @paolinomanghi will look into resolving the mislabeling. Once that happens the change will propagate the package automatically.

CraigGin commented 2 years ago

Great, thanks

lwaldron commented 2 years ago

Pinging @paolinomanghi - would be great to fix this before the Bioconductor 3.15 release.