Question regarding the NA values

[Jeon, Hyeongseon]

Dear cbioportal manager,

 

I am a postdoctoral researcher and doing some preliminary research using cbioportal dataset.

I really appreciate your efforts and works, which is helping a lot of researchers.

 

I have a question about phosphoprotein_quantification.txt dataset.

In the meta dataset, description says it is phosphoprotein site level expression data measured with mass spectrometry by the CPTAC.

In the site expression data, there are many NA values.

Could you let me know what NA values mean?

OR, can I get more information about the measurement?

 

Best,

Sammy

 

 

Hyeongseon Jeon, Ph.D.
Postdoctoral Scholar

The Ohio State University
Chung Lab, Department of Biomedical Informatics, College of Medicine
Biomedical Research Tower
460 W 12th Ave, Columbus, OH 43210

 

 

[Matthijs Pon]

Hi Hyeongseon,

Thanks for reaching out! NA values in data files mean that they were either not measured or not made available by the original authors of the dataset. I'm unsure which specific dataset you are inquiring about, but if there is no information provided on the process in the meta file (meta_phosphoprotein...) it should be available in the paper where the dataset originated from. You can find the associated paper in two ways: on the cbioportal website, there is a linked citation in both the overview (book icon) and study-view page (see images). If you're looking at the raw data, the 'meta_study.txt' file contains a line starting with 'pmid: ', the values here are the pubmed IDs of any associated publications.

I hope this answers your question. If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal google groups.

With kind regards, Matthijs Pon

Data Engineer cBioPortal

E matt...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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