Hi, All

i am working in pharmaceuticals in japan.

i am so new to Bioconductor, now i am thinking to download data from TCGA database using TCGAbiolinks.

if i tryed to download from TCGA web site, i can download files, however if i tryed to download via TCGAbiolinks,

especially function "TCGAdownload", i failed to download data.

would you mind telling me how to download using TCGAdownload ?

Thanks in advance.

> TCGAdownload(datQuery,type = "rsem.genes.results",samples = "TCGA-A7-A0CH-11A-32R-A089-07")
Error in function (type, msg, asError = TRUE)  :
  Failed to connect to tcga-data.nci.nih.gov port 443: Timed out

The message "Failed to connect to tcga-data.nci.nih.gov port 443: Timed out" happens when the open-access http directory is not reachable for some reason (server is down for maintenance). 

The code below is working for me:

datQuery <- TCGAquery(tumor = "BRCA",
                      platform = "IlluminaHiSeq_RNASeqV2",
                      samples =  "TCGA-A7-A0CH-11A-32R-A089-07")
TCGAdownload(datQuery,type = "rsem.genes.results",samples = "TCGA-A7-A0CH-11A-32R-A089-07")
data <- TCGAprepare(datQuery,type = "rsem.genes.results",samples = "TCGA-A7-A0CH-11A-32R-A089-07", dir = ".")

Hi All, 

i am trying to analyze tcga brca data.

it is raw microarray data

raw intensities

access closed

i am trying to using tcga biolink with commands gdcquery, gdcdownload, gdcprepare.

it looks like gdc prepare not working.

is there any other package to use for further analysis?

platform Affymetrix SNP Array 6.0

would you please help me?

Thank you

ugandhar