Hi, all.

i am very new to Bioconductor, and now i am planning to analysis using TCGAbiolinks.

regarding the data of Genome_Wide_SNP_6, i was not able to acquire the data via TCGAbiolinks.

TCGAdownload worked well, but as a next step,  TCGApreapre did not work.

if you know it, would you mind teaching me about how to write script for  TCGA prepare ?

thanks in advance .

TCGAdownload(data = datQuery2,
             path = "C:/Users/......./TCGA database",
             samples =c(dataSmTP2,dataSmTN2))

dataAssyCNV <- TCGAprepare(query = datQuery2,
                        dir = "C:/Users/....../TCGA database",
                        save = TRUE,
                        type=".hg19.seg.txt",
                        summarizedExperiment = TRUE,
                        samples = c(dataSmTP2,dataSmTN2),
                        filename = paste0(cancer,"_","Genome_Wide_SNP_6" ,".rda"))

I believe the bug was solved. Could you test the new version from github? I'll foward to bioconductor, but it will take one or two days to be there.

Also, for platform  Genome_Wide_SNP_6  the possible types (for download and prepare) are:

• hg18.seg
• hg19.seg
• nocnv_hg18.seg
• nocnv_hg19.seg

Example code: