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Question: Data download via TCGAbiolinks
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gravatar for maedakus
16 months ago by
maedakus10
maedakus10 wrote:

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

 

 

ADD COMMENTlink modified 4 days ago by ugandhar.ch10 • written 16 months ago by maedakus10

Have you thought about using a graphical interface instead?

ADD REPLYlink written 16 months ago by Dario Strbenac1.3k
1
gravatar for tiagochst
16 months ago by
tiagochst80
Brazil
tiagochst80 wrote:
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 = ".")

 

 

 

ADD COMMENTlink written 16 months ago by tiagochst80
0
gravatar for ugandhar.ch1
4 days ago by
ugandhar.ch10 wrote:

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

ADD COMMENTlink written 4 days ago by ugandhar.ch10
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