Question: Error in GDCprepare in TCGAbiolinks
0
gravatar for sandhana.krishnan
21 months ago by
sandhana.krishnan0 wrote:

Hi, I have used the code below to download and prepare data from TCGA using the TCGAbiolinks package for R. library("TCGAbiolinks") query <- GDCquery(project = "TCGA-PRAD", data.category = "DNA Methylation", experimental.strategy = "Methylation Array")

GDCdownload(query, chunks.per.download = 5)

data <- GDCprepare(query) return(data)

After the download is completed, I get the error.

data <- GDCprepare(query)

Read 485577 rows and 11 (of 11) columns from 0.132 GB file in 00:00:03=============================================| 100%

Read 485577 rows and 11 (of 11) columns from 0.132 GB file in 00:00:04

Starting to add information to samples

=> Add clinical information to samples

Error: lexical error: invalid char in json text. <respons (right="" here)="" ------^<="" p="">

return(data)

Error: no function to return from, jumping to top level

Can anyone help me sort this error? Thanks in advance Sandhanakrishnan

R tcgabiolinks • 857 views
ADD COMMENTlink modified 21 months ago by theresa10 • written 21 months ago by sandhana.krishnan0
0
gravatar for theresa
21 months ago by
theresa10
theresa10 wrote:

tiagochst answered here:

https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/65

ADD COMMENTlink written 21 months ago by theresa10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1300 users visited in the last hour