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")

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

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