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I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal A, luminal B, HER2-like, basal-like).

However, since I don't know the portal, I'm having problems in associate the EXP data and the label.

I could get the label either by using the old TCGA-barcode and use a dictionary I already have from an article (but I don't know how to get the barcode from the portal / API) or by using clinical data (but I don't know how to find metadata that link the EXP and the clinical data).

Is there anyone more used to the portal who could help me?

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    $\begingroup$ Your question doesn't give enough details for even someone familiar with this portal to try and help, I think. Do you have an example of a dataset you want to interrogate, and how it is deficient in the details you require? $\endgroup$
    – sjcockell
    Commented Jul 25, 2018 at 13:24

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I personally find the GDC portal not very user-friendly. However, some of the data is available from other sources. For example, you can download TCGA-BRCA FPKMs and phenotypes from UCSC Xena here: https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)

All the sample info is already combined and the labels are the classic TCGA barcodes.

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These data are in Experiment Hub in Bioconductor

library(curatedTCGAData)
brcaRNA <- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
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  • $\begingroup$ If you could expand your answer to explain how this helps to link data from the samples to each sample it would make a great answer $\endgroup$
    – llrs
    Commented Jan 9, 2019 at 11:42

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