Raw counts from RSEM

[Ashish Yeri]

Hi,

First of all, I would like to say how amazing the cbioportal resource is. Thank you very much for all of this wonderful data. 

My question is how to get access to the raw RSEM counts fior the TCGA rnaseq data. On cbioportal I have access to the RNA_Seq_v2_expression_median, which I gather is the raw counts scaled by the 75th percentile of the genes in each sample. 

We have performed RNASeq on a set of samples and I'd like to know how similar our samples are transcriptomically to the AML TCGA datasets.  If I can get the raw counts so I could normalize them to make sure there are no sequencing depth issues with our set of samples. Please let me know if there is a way to download the raw RSEM counts. Any help is greatly appreciated. 

Best regards,

Ashish Yeri

[David Higgins]

Hi Ashish,

Unfortunately, the portal only contains gene-level processed data. Raw and probe-level data for data sets are available via NCBI GEO, dbGaP or through the GDC. See the cancer type description on the main query page or refer to the original publication for links to the raw data.

Our FAQs page has more information about how our mRNA Seq data is processed: https://docs.cbioportal.org/1.-general/faq#rna  

Best,

David Higgins

Scientific Community Program Manager

Center for Data-Driven Discovery in Biomedicine (D3b)

Children's Hospital of Philadelphia, USA