Question: TCGAbiolinks download error
0
gravatar for Björn
14 months ago by
Björn40
Björn40 wrote:

I used following commands to download -"Data.category- Biospecimen"

bio_query <- GDCquery(project = "TCGA-PRAD", data.category = c("Biospecimen"))
GDCdownload(bio_query)

but received following error

Error in GDCdownload(bio_query) : We can only download one data type. Please use data.type argument in GDCquery to filter results.

My aim is to get the biospecimen, clinical.info="sample" data . How to solve the problem ? How to get the normal sample data for the TCGA-PRAD ?

tcga R tcgabiolinks • 590 views
ADD COMMENTlink modified 14 months ago by zx87547.9k • written 14 months ago by Björn40
2
gravatar for mathias.heydt
14 months ago by
mathias.heydt90 wrote:

You need to add your data.type, that's all ;):

bio_query <- GDCquery(project = "TCGA-PRAD", data.category ="Biospecimen", data.type="Biospecimen Supplement")

Basically, if you specify Biospecimen in your data category in the TCGA repository, you'll see that it contains two datatypes. You had to specify which one you need. And that applies to everything you want to download, just go to the repository and make your query as specific as needs be ;)

ADD COMMENTlink modified 14 months ago • written 14 months ago by mathias.heydt90
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