TCGA-BRCA downloading issue by GDCquery

Question

[H. Z. Amini]

Hi, I'm going to download the "TCGA-BRCA" with the following command in Rsudio, but I got an error. Would you please help me out ? Thank you!

query.seq <- GDCquery(project = "TCGA-BRCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantification", sample.type = c("Primary Tumor","Solid Tissue Normal"), workflow.type = "HTSeq - Counts")

GDCdownload(query.seq)
seq.brca <- GDCprepare(query = query.seq, save = TRUE, save.filename = "brca-RNAseq-Counts.rda", summarizedExperiment = TRUE)

Error

Error in GDCprepare(query = query.seq, save = TRUE, save.filename = "brca-RNAseq-Counts.rda", : I couldn't find all the files from the query. Please check if the directory parameter is right or GDCdownload downloaded the samples.

[Nitin Narwade]

I guess you forgot to creat a data directory. The default value is GDCdata, you can check it whether it has created or not. If not then you can try and create it manually.

[Hamid Ghaedi]

H. Z. Amini Please stop cross posting: https://support.bioconductor.org/p/9137518/