Answers.Body: <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>
  
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Answers.CreationDate: 2021-12-30T17:48:32.293Z
Answers.Text: Thank you for your answer. This is an essential information for a user of this data. I wonder why this information on the ICGC website itself though. I found a page describing the columns on github https://github.com/icgc-dcc/dcc-docs/blob/master/docs/dictionary/release-20/sequencing-based-gene-expression-expseq-primary-file-p.md. It does not explicitly say what `normalized_read_count` are. Also the page corresponds to one of the older release (20), not the current one (28).
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Answers.CreationDate: 2018-01-10T15:36:00.090Z
Answers.Text: Glad you could find it yourself! Many thanks for posting the answer
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Answers.CreationDate: 2018-01-10T14:57:21.637Z
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Answers.UserDisplayName: Gregor Sturm
Body: <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>
  
Tags: <rna-seq><public-databases>
Title: What is the ICGC normalized_read_count?
ThreadText: # What is the ICGC normalized_read_count?
  
  (Asked by: username_0 on 2018-01-08)
  
  I downloaded gene expression data (`exp_seq`) from the [ICGC file browser](https://dcc.icgc.org/releases/current/Projects/BRCA-US).
  
  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.
  
  **Tags:** rna-seq, public-databases
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-01-10. Score: 5 | Accepted answer
  
  By reading [this thread](http://seqanswers.com/forums/showthread.php?t=42911) 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](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323)
  * `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.
  
  > **Comments:**
  > **username_2**: Glad you could find it yourself! Many thanks for posting the answer  
  > **username_1**: Thank you for your answer. This is an essential information for a user of this data. I wonder why this information on the ICGC website itself though. I found a page describing the columns on github https://github.com/icgc-dcc/dcc-docs/blob/master/docs/dictionary/release-20/sequencing-based-gene-expression-expseq-primary-file-p.md. It does not explicitly say what `normalized_read_count` are. Also the page corresponds to one of the older release (20), not the current one (28).  
  
  ---
  
  