1

How do I convert TCGA RNA normalized_count the TPM values as calculated for GTEx. Right now the TPM values on GTEx are dramatically smaller than the values of TCGA.

The tables that I am looking at are on BigQuery are:

`isb-cgc.TCGA_hg19_data_v0.RNAseq_Gene_Expression_UNC_RSEM`

and 

`isb-cgc.GTEx_v7.gene_tpm`

Thanks, eilalan

eilalan
  • 669
  • 4
  • 20

1 Answers1

2

To convert between the two scales, you'll need the raw read counts. For TCGA data, raw read counts are available for the hg38 dataset in the table isb-cgc:TCGA_hg38_data_v0.RNAseq_Gene_Expression. ISB-CGC is currently updating the TCGA hg19 RNAseq table to include raw read counts. ISB-CGC will also make available an updated GTEx table to v8.

isb-cgc-user-support
  • 21
  • 2