TCGA-BRCA downloading issue by GDCquery
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.
• 3,149 views
•
link
updated
by
Ram
•
written
by
H. Z. Amini •
•
written
by
H. Z. Amini •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
TCGA RNAseq
written by Rob •
-
downloading RNA seq data
written by Rob •
-
Differential expression analysis of TCGA data based on tumor staging
written by txtbookir •
-
TCGA data Query (GDCquery): external_gene_name " are missing
written by H. Z. Amini •
-
TCGAbiolinks HT-Seq count
written by Rob •
-
HT-Seq count data coding gene
written by Rob •
-
HT-Seq count data coding gene
written by Rob •
-
GDCprepare stop working for some unknown reason
written by ansari.sarabio •
-
Matched Paired Tumour-Normal DEA of BRCA using data downloaded using TCGAbiolinks
written by aluesley1 •
-
TCGAbiolinks TCGA-BRCA RNA-seq clinical data
written by Matina
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.H. Z. Amini Please stop cross posting: https://support.bioconductor.org/p/9137518/