Question: TCGA biolinks GDCdownload file sizes mismatch
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gravatar for Nopstoc
2.6 years ago by
Nopstoc0
INBIOMED, Buenos Aires, Argentina
Nopstoc0 wrote:

Hello!

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] 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

 resu1$definition

I get

[1] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor" [5] "Primary solid Tumor" "Primary solid Tumor" "Solid Tissue Normal" "Solid Tissue Normal" [9] "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

Juan

R tcgabiolinks • 1000 views
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