Clarification on mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)

[soumaya rafii]

Dear cBioPortal Support Team,

I hope this message finds you well.

I am currently working with the mRNA expression data from the TCGA PanCancer Atlas study. I have downloaded the RNA-seq V2 RSEM data (Batch normalized from Illumina HiSeq_RNASeqV2) from your portal. 

To ensure the accuracy of my downstream analyses, particularly deconvolution using CIBERSORT, I need to confirm the type of expression values provided in this dataset. Could you please clarify whether the values in the RNA-seq V2 RSEM dataset are in TPM (Transcripts Per Million) or FPKM (Fragments Per Kilobase of exon model per Million reads mapped)?

Thank you very much for your assistance and for providing such a valuable resource to the research community. I look forward to your response.

Best regards,

Soumaya Rafii, PhD

Cytogenetics laboratory manager

Mohammed VI University of Sciences and Health. 

[JJ Gao]

Hi Soumaya,

The TCGA PanCancer Atlas studies use RSEM normalized data [1] followed by batch correction [2].

[1] https://translational-medicine.biomedcentral.com/articles/10.1186/s12967-021-02936-w

[2] https://www.sciencedirect.com/science/article/pii/S0092867418303027?via%3Dihub#sec4.4.5

Best,

-JJ

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