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hms-dbmi / OncoThreads

OncoThreads longitudinal cancer genomics visualization project.
http://oncothreads.gehlenborglab.org
MIT License
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sample intermittently has no data #223

Closed tmazor closed 4 years ago

tmazor commented 4 years ago

P24_pri loads without data semi-consistently. Screenshot below is from "Low-Grade Gliomas with CNA and mRNA-seq". I've also see this with "Low-Grade Gliomas with all data types", so it's not study specific. If I re-load the study, the data is there.

I've seen this happen multiple times, on different days, and always with that one sample.

image

ThHarbig commented 4 years ago

This is because of an error in the data itself in all low grade glioma studies. A sample has been assigned to the wrong patient in the timeline SPECIMEN file. As this wrong assignment is not consistent in the other files/api calls, data cannot be associated with that sample of the patient. This error only occurs sometimes because if there are multiple samples per patient in a timepoint we chose one randomly.

tmazor commented 4 years ago

Ohhh yes I see this in the data now... there's a sample from P26 which is assigned to P24 by mistake in that one file. It is like this in the original data files which I used as the basis for every version of the study. Thanks for figuring that out!