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14 months ago by
ks2002p0
ks2002p0 wrote:

Dear Bioconductor,

I am working with TCGA data anaylsis. I want to download and analyze the TCGA data ( Project : TCGA-THCA).

using your TCGAbioconductort package, I could do practice in TCGA-LGG, GBM well.

but I can't do it again in TCGA-THCA because I don't know how to get the barcodes like as your protocol article(TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages https://www.ncbi.nlm.nih.gov/pubmed/28232861). and I have some questions.

Q1. can I know how to get the TCGA-THCA barcode numbers which should be in there as like bold letters in example below?

11 met.gbm.450 <– GDCprepare(query = query.met.gbm,
12                         save = TRUE,
13                         save.filename = "gbmDNAmet450k.rda" ,
14                         summarizedExperiment = TRUE)
15 query.met.lgg <– GDCquery(project = "TCGA–LGG",
16                              legacy = TRUE,
17                              data.category = "DNA methylation ",
18                        platform = "Illumina Human Methylation 450",
19                        barcode = c("TCGA–HT–7879–01A–11D–2399–05", "TCGA–HT–8113–01A–11D–2399–05" )
)]

And I want to know the detailed meaning of each column in the barcode too, if possible.

Example of the above barcode : TCGA–HT–7879–01A–11D–2399–05

I think they might be matters of TCGA database but I can't find it anywhere. so please help me to start the anaylsis.

Thank you for your good tutorial here!

Sincerely,

Park

modified 14 months ago by rasnajacob480 • written 14 months ago by ks2002p0
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14 months ago by
Denali
Steve Lianoglou12k wrote:

The meaning of the barcodes are explained quite well here.