TPM for TCGA and GTEX RNA

Question

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

Answer 1

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.