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waldronlab / curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataCuration/
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days_from_first_collection inaccuracies in HMP_2019_ibdmdb #76

Closed mruehlemann closed 10 months ago

mruehlemann commented 10 months ago

Hi,

I think there some of the values in the days_from_first_collection variable are incorrect in the HMP_2019_ibdmdb study. When comparing the values in the curatedMetagenomicData package and the sampling dates obtained from the corresponding QIITA dataset (https://qiita.ucsd.edu/study/description/11484), the numbers don't fit, e.g. see below for subject_id == M2048

image

lwaldron commented 10 months ago

@paolinomanghi can you look into this?

paolinomanghi commented 10 months ago

Hi @mruehlemann , sorry for the long absence, and thanks for pointing this error out! So, I confirm there was an issue: after filtering out the metagenomic samples from the original table the number of days between timepoints do not much exactly anymore the correct day span, or at least this is what I think. Using the sampling date, this should be solved.

An amended version has been pushed now. I'm closing this, as seems correct now. Thanks