text: user1656: I downloaded gene expression data (exp_seq) from the ICGC file browser. 
  For each sample and gene, the file contains a normalized_read_count. 
  What is that value? I couldn't find any information on the ICGC website. The values are definitly too low for TPM. 
  
  user1656: By reading this thread on seqanswers and by comparing the data to TCGA, I figured out
  
  raw_read_count is the read count which you use as input for e.g. DESeq2. It has been estimated using RSEM
  normalized_read_count is equivalent to the scaled_estimate from TCGA. This is the estimated fraction of transcripts made up by a given gene, as estimated by RSEM. Multiplying this value with 1e6 yields the TPM. 
  
  
original_text: 1656: <p>I downloaded gene expression data (<code>exp_seq</code>) from the <a href="https://dcc.icgc.org/releases/current/Projects/BRCA-US" rel="noreferrer">ICGC file browser</a>. </p>
  
  <p>For each sample and gene, the file contains a <code>normalized_read_count</code>. </p>
  
  <p>What is that value? I couldn't find any information on the ICGC website. The values are definitly too low for TPM. </p>
   1656: <p>By reading <a href="http://seqanswers.com/forums/showthread.php?t=42911" rel="noreferrer">this thread</a> on seqanswers and by comparing the data to TCGA, I figured out</p>
  
  <ul>
  <li><code>raw_read_count</code> is the read count which you use as input for e.g. <code>DESeq2</code>. It has been estimated using <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323" rel="noreferrer">RSEM</a></li>
  <li><code>normalized_read_count</code> is equivalent to the <code>scaled_estimate</code> from TCGA. This is the <em>estimated fraction of transcripts made up by a given gene</em>, as estimated by RSEM. Multiplying this value with 1e6 yields the TPM. </li>
  </ul>
  