Hi,

I know cghub is down and TCGAbiolinks get changed a lot. It says in the manual it is working with 450k data, but it is not.

query.GBM<- GDCquery(project = "TCGA-GBM",
                      data.category = "DNA methylation", 
                      platform = "Illumina Human Methylation 450", 
                      legacy = TRUE)

str(query.GBM$results)

## download data
GDCdownload(query.GBM, directory = "GBM_meth")

GDCdownload will download: 3.300125655 GB compressed in a tar.gz file
Downloading as: Tue_Sep_20_16_31_55_2016.tar.gz
Error in file(con, "rb") : cannot open the connection
In addition: Warning message:
In file(con, "rb") :
  cannot open file 'Tue_Sep_20_16_31_55_2016.tar.gz': No such file or directory

The file is missing somehow?

Thanks!

Ming

Hi,

Your code is right. There might be an error connection with  the GDC API. Unfortunately, this problem happens very often.

Maybe using client method or downloading less samples at a time will solve the problem.

# For client method

GDCdownload(query_methy, method = "client", directory = "GBM_meth")

# For less sampleslibrary(TCGAbiolinks)

query.GBM<- GDCquery(project = "TCGA-GBM",
                     data.category = "DNA methylation", 
                     platform = "Illumina Human Methylation 450", 
                     legacy = TRUE)

n <- nrow(query.GBM$results[[1]])
step <- 5
for(i in 0:(n/step)){
    end <- ifelse(((i + 1) * step) > n, n,((i + 1) * step))
    query_methy.aux <- query.GBM
    query_methy.aux$results[[1]] <- query_methy.aux$results[[1]][((i * step) + 1):end,]
    GDCdownload(query_methy.aux, method = "api", directory = "GBM_meth")
}
GDCdownload(query.GBM, method = "api", directory = "GBM_meth") # just to be sure everything was downloaded
met <- GDCprepare(query = query_methy,
                  save = TRUE,
                  save.filename = paste0(cancer,"_DNAmethylaltion_450k.rda"),
                  summarizedExperiment = TRUE)

If the problem continues, could please you send your sessionInfo() ?

Best regards,

Tiago