I'm new to bioinformatics, and wanted to get some array data from TCGA, using TCGA biolinks.
I ran a query for 12 files, 2 groups of 6 samples with the same type of cancer, and when I ran GDC download I get this confusing information:
GDCdownload(query) GDCdownload will download 12 files. A total of 119.416574 MB Downloading as: Fri_Nov_25_09_39_55_2016.tar.gz Downloading: 31 MB  1
the download stops at 31MB always. different chunks get me the same final size of 31 MB (for example in chunks of 2 files, I get the message that each chunk is 20 mb but they get completed at 5.1MB. setting chunks of 1 file each makes it so that I get only one downloaded and then an error message.
I tried working with the data as it downloaded but keep getting errors, I'm guessing due to missing information
Here's the query and graph for reference:
query2 <- GDCquery(project = "TCGA-BRCA", data.category = "DNA Methylation", platform = "Illumina Human Methylation 27", barcode = casos) # casos is a character vector with the barcodes of the cases i wanted
and the error message
Group1:solid tissue normal Group2:primary solid tumor Error in TCGAanalyze_DMR(resu1, groupCol = "definition", group1 = "solid tissue normal", : Sorry, but solid tissue normal has no samples In addition: Warning message: In any(rowSums(!is.na(assay(data)))) : coercing argument of type 'double' to logical
if I run
 "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"  "Primary solid Tumor" "Primary solid Tumor" "Solid Tissue Normal" "Solid Tissue Normal"  "Solid Tissue Normal" "Solid Tissue Normal" "Solid Tissue Normal" "Solid Tissue Normal"
Showing that groupCol is actually getting a column that can be splitted in 2.
Hoping to get some help, thank you in advance