Question

TCGA: clinical data and expression data

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641549298 • 0

@641549298-24146

Last seen 4.2 years ago

Here I have clinical data which each line is a case, its number is TCGA-xxxx-xx(only three fields，such as TCGA-A6-2670).

But the expression data have multiple samples of a case (such as TCGA-A6-2670-01A-02R-0821-07, TCGA-A6-2670-01A-02D-0820-05, TCGA-A6-2670-01A-02T-0822-13 and so on)？

So how can I match every sample to the only one clinical record. Or do all cancer samples correspond to the same clinical case？

(I have checked the clinical data, there's no information can match the sample)

Thank You Very Much！

microarray annotation cancer • 2.6k views

ADD COMMENT • link updated 22 months ago by Sharif • 0 • written 4.2 years ago by 641549298 • 0

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Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expression data against each patient's TCGA barcode (such as TCGA-A6-2670-01A-02R-0821-07). As I have to do the differential expression of gene analysis and need clinical data also, I downloaded "Race" data also by using Bioconductor packages. But I got race data against the patient barcode (TCGA-xxxx-xx, only three fields，such as TCGA-A6-2670). How I will determine which patient Id (TCGA-xxxx-xx) corresponds to which TCGA barcode (TCGA-A6-2670-01A-02R-0821-07)? or now how I will add the TCGA barcode to my clinical data??

ADD REPLY • link 22 months ago Sharif • 0

score 1 · Answer 1 · 2020-09-14

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Kevin Blighe ★ 4.0k

@kevin

Last seen 29 days ago

Republic of Ireland

Your question is not related to any Bioconductor package.

In this case, you can assume that the clinical record for TCGA-A6-2670 applies equally to all samples of the form: TCGA-A6-2670-XXX-XXX-XXXX-XX.

Please take time to review the TCGA barcode: https://www.biostars.org/p/313063/#313066

Kevin

ADD COMMENT • link 4.2 years ago Kevin Blighe ★ 4.0k

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Thanks！！

ADD REPLY • link 4.2 years ago 641549298 • 0

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I also want to ask a question: Is it possible that different samples of the same case are sampled at different cancer stages (multiple sampling), which will cause a problem that one clinical record cannot correspond to the correct sample.

ADD REPLY • link 4.2 years ago 641549298 • 0

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I do not know the answer for definite, but I think that it is 'no'. You could contact the NCI GDC to try to find out for definite ( https://gdc.cancer.gov/contact-us ) or consult the project documentation for TCGA

ADD REPLY • link 4.2 years ago Kevin Blighe ★ 4.0k

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Keep in mind that you can also look up (search for) barcodes at the GDC Data Portal and, in this way, see updated clinical information for any specific sample..

ADD REPLY • link 4.2 years ago Kevin Blighe ★ 4.0k