Question: TCGA biolinks data download
0
gravatar for maedakus
3.5 years ago by
maedakus10
maedakus10 wrote:

Hi,

when downloading data from TCGA dabase using Biolinks, i got an error as below.

if you know how to solve this, would you mind telling me ?

thanks in advance !

 

TCGAdownload(data = datQuery2,
             path = "D:/...../TCGA database",
             type = dataType,
             samples =c(dataSmTP,dataSmTN))
Error: invalid multibyte string at '<a0>'

*****************************************************

cancer <- "COAD"
PlatformCancer <- "IlluminaHiSeq_RNASeqV2"
dataType <- "rsem.genes.results"
pathCancer <- paste0("D:/....../TCGA database")

datQuery2 <- TCGAquery(tumor = cancer, platform = PlatformCancer, level = "3") 
lsSample <- TCGAquery_samplesfilter(query = datQuery2)

# get subtype information
dataSubt <- TCGAquery_subtype(tumor = cancer)

# Which samples are Primary Solid Tumor
dataSmTP <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2,
                                  typesample = "TP")
# Which samples are Solid Tissue Normal
dataSmTN <- TCGAquery_SampleTypes(barcode = lsSample$IlluminaHiSeq_RNASeqV2,
                                  typesample ="NT")

 

 

 

 

tcgabiolinks • 1.0k views
ADD COMMENTlink modified 3.5 years ago by tiagochst150 • written 3.5 years ago by maedakus10
Answer: TCGA biolinks data download
0
gravatar for waltwu512
3.5 years ago by
waltwu5120
waltwu5120 wrote:

Hi maedakus,

I guess it is because TCGAdownload download TCGA data directly from TCGA portal, which is currently down for maintenance. Please check https://tcga-data.nci.nih.gov/.

Maybe you can download the data you need from Firehose, you can take a look at it.

Hope this helps you :)

Walt Y.L. Wu

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by waltwu5120

thank you so much for telling me , i will try again after the recovery of database.

ADD REPLYlink written 3.5 years ago by maedakus10
Answer: TCGA biolinks data download
0
gravatar for tiagochst
3.5 years ago by
tiagochst150
Brazil
tiagochst150 wrote:

Hi,

The problem is related to the maintenance of TCGA data portal. 

As we are not sure it will comeback, we are rewriting the code to make TCGAbiolinks use GDC database instead the old TCGA data portal.

There should be an update in the coming weeks in Bioconductor repository.

Best regards,

Tiago

ADD COMMENTlink written 3.5 years ago by tiagochst150

dear tiago,

thank you so much for telling me , i am looking forwards to using new TCGAbiolinks.

 

ADD REPLYlink written 3.5 years ago by maedakus10
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