Study View: Clinical data tab receives no data when there is no sample-level attribute for selected samples about cbioportal

[MatthijsPon]

Hi Iris,

I've never experienced this to be a requirement for loading sample data. Which cBioPortal version are you using?

[I-Huitink]

Hi Matthijs,

I'm using cBioPortal 5.4.7.

To elaborate on this issue: I have a dataset with clinical patient data only. In order to be able to upload this data to cBioPortal, I created the clinical patient data file in the regular way and the clinical sample data file with only two columns, PATIENT_ID and SAMPLE_ID. The validation and importing step were successfully completed and I'm able to see the data on the Summary tab:

But then the Clinical Data tab is just empty:

I tried figuring out what was the problem by adding/removing columns at patient level and sample level. Then I noticed that the problem was solved after adding 'SAMPLE_TYPE'.

If you need any more details, I'm happy to provide them.

Best,
Iris

[MatthijsPon]

Hi Iris,

Thank you for the information. Unfortunately, I cannot reproduce your issue on v5.4.7. Would you be able to provide a small mock dataset which produces this error for you?

Kind regards,
Matthijs

[I-Huitink]

data_clinical_patient.txt
data_clinical_sample_ELABORATE_AND_WORKING.txt
data_clinical_sample.txt
meta_clinical_patient.txt
meta_clinical_sample.txt
meta_study.txt

Hi Matthijs,

Yes, see attached. I also added an example file that is preventing the issue.

Best,
Iris

[MatthijsPon]

Hi Iris,

I have been able to reproduce your issue and I am looking into the possibility of resolving it. For the time being, any extra column in data_clinical_sample.txt (next to patient_id and sample_id) should resolve the issue. It's not dependent on SAMPLE_TYPE, but sample type might be a good column to use as a temporary remedy.

Thank you for the help in identifying the issue. I'll let you know once there is a resolution!

Best,
Matthijs

[I-Huitink]

Hi Matthijs,

Thanks for the update, looking forward to the final solution!

Best,
Iris