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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.

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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.
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  • $\begingroup$ Glad you could find it yourself! Many thanks for posting the answer $\endgroup$
    – llrs
    Jan 10 '18 at 15:36

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