TPM values from TCGA datasets

Question

[rodolfo.peacewalker]

Hello,

I am dealing with an issue at the moment of running TIMER for estimation of immune infiltration. Following the file requirements, the input expression file should be TPM-normalized without log2 transformation. For this, I downloaded the GDC-TCGA LUAD dataset from Xena Browser, retrieved the HTSeq Counts, and removed the log2 transformation. My question is about the possibility to normalize using TPM from this point. I am aware that TPM normalization is indicated for transcripts instead genes. Also, is there a way to download TPM valued of TCGA datasets?

Thanks in advance,

Rodo

Answer 1

[jv]

Xena provides transcript-level TPM values, see the options under transcript expression RNAseq at https://xenabrowser.net/datapages/?cohort=TCGA%20TARGET%20GTEx

[rodolfo.peacewalker]

Thanks for your suggestion, I will use it to get all the samples from LUAD.