TCGA clinical data: Multiple measure of response columns in merged clinical xml file.

Question

[vibhamishra017]

Hi all, I really need some help. I am trying to download clinical data (xml files) for TCGA-BRCA project using TCGAbiolinks package and then merged all clinical files such as follow up, drug... using following command as suggested in TCGAbiolinks tutorial, which worked fine -

aux <- GDCprepare_clinic(query, clinical.info = i)

Now I got all the clinical xml files columns in one excel file (attached some cropped columns).

My question is there are two columns with similar information like measure of response.x and measure of response.y and both contain different treatment response information like complete response and other with stable disease. Which column should i consider for final study? for one patient what should i consider whether the patient completely responded to the treatment or the disease is stable? Any help would be really appreciated. I'm literally stuck in my study.

Answer 1

[Zhenyu Zhang]

I don't know how tcgabiolinks merges them, but this looks like a typical R merging behavior when two data frames to be merged have columns of the same name in addition to the key. I am not sure if this results from two independent treatment, or two different tumor events from the same patient. I suspect the later because I assume tcgabiolinks should be able to handle multiple treatment well. You should download the XML of your first patient to check the details.

As to how to use the data, finding the date of the treatment could be helpful. Also if the edge case is rare, you can just remove this patient for simplicity and cleanness.