TCGA biolinks data download
2
0
Entering edit mode
maedakus ▴ 10
@maedakus-9484
Last seen 7.6 years ago

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 • 2.2k views
ADD COMMENT
0
Entering edit mode
waltwu512 • 0
@waltwu512-11111
Last seen 7.7 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
@tiagochst-7121
Last seen 9 months ago
Miami, US

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 COMMENT
0
Entering edit mode

dear tiago,

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

 

ADD REPLY

Login before adding your answer.

Traffic: 879 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6