0
$\begingroup$

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?

Improve this question
$\endgroup$
1
  • 2
    $\begingroup$ 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
    Jul 25, 2018 at 13:24

2 Answers 2

Reset to default
1
$\begingroup$

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.

Improve this answer
$\endgroup$
2
1
$\begingroup$

These data are in Experiment Hub in Bioconductor

library(curatedTCGAData)
brcaRNA <- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
Improve this answer
$\endgroup$
1
  • $\begingroup$ 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
    Jan 9, 2019 at 11:42

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.