text: user3114: 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?
  
  user35: 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.
  
  user3939: These data are in Experiment Hub in Bioconductor
  library(curatedTCGAData)
  brcaRNA <- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
  
  
original_text: 3114: <p>I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (<a href="https://portal.gdc.cancer.gov/repository" rel="nofollow noreferrer">https://portal.gdc.cancer.gov/repository</a>) to classify breast cancer subtypes (luminal A, luminal B, HER2-like, basal-like).</p>
  
  <p>However, since I don't know the portal, I'm having problems in associate the EXP data and the label.</p>
  
  <p>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).</p>
  
  <p>Is there anyone more used to the portal who could help me?</p>
   35: <p>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: <a href="https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)" rel="nofollow noreferrer">https://xenabrowser.net/datapages/?cohort=GDC%20TCGA%20Breast%20Cancer%20(BRCA)</a></p>
  
  <p>All the sample info is already combined and the labels are the classic TCGA barcodes.</p>
   3939: <p>These data are in Experiment Hub in Bioconductor</p>
  
  <pre><code>library(curatedTCGAData)
  brcaRNA &lt;- curatedTCGAData("BRCA", "RNASeq2GeneNorm", dry.run = FALSE)
  </code></pre>
  