0
3.5 years ago by
maedakus10
maedakus10 wrote:

Hi,

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

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


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

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")

modified 3.5 years ago by tiagochst150 • written 3.5 years ago by maedakus10
0
3.5 years ago by
waltwu5120 wrote:

Hi maedakus,

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

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

0
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

dear tiago,

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