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Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values

How to convert data_mrna_seq_v2_rsem.txt having rsem.genes.normalized_results file from LUSC (Lung Squamous cell carcinoma) TCGA data into TPM values?

tpm rna-seq cbioportal rsem
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updated by Sachin • Sachin • written by shakyaram079 • shakyaram079

Can you give us a link to the dataset please?

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written by Ram Ram

Hi, I have the same question. You can find the dataset in here.

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written by songyeon0425 • songyeon0425

I think those are simply log2-transformed TPM values. It's log2(TPM+x) where x is a pseudocount. I think x is either 1 or 0.001. In any case, just reverse-log2 transform it, and if you did it correctly, the sum of the recovered counts across all transcripts/genes within any given sample should be 10^6.

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written by dsull dsull

Thank you for your reply. But I'm not sure whether it was log2-transformed or not because the range of values is too large. For example, the maximum value in the LUSC TCGA data is 1,737,510 for the ADAM6 gene in the TCGA-85-A513-01 sample. Can you give me a description of it?

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written by songyeon0425 • songyeon0425

The URL you linked to only has "batch normalized" expression. Unfortunately, there is no way to undo batch normalization to recover TPM values.

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written by dsull dsull

Is this query resolved? I am also confused that how to obtain TPM from these data_mrna_seq_v2_rsem.txt files

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written by Sachin • Sachin

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