RNA-seq raw data transformation

[Marina Oteiza]

Dear cBioPortal team,

First of all, I would like to thank you for the outstanding work you have accomplished with cBioPortal. Your platform has been an invaluable resource for the research community, providing comprehensive and accessible cancer genomics data.

I'm a college student doing a summer internship in  Vall d'Hebron Instituto de Oncología (VHIO) and I'm currently working with RNA-seq raw data form the dataset Prostate Adenocarcinoma (TCGA, PanCancer Atlas). 

I have downloaded the raw counts data from GDC but I'm struggling trying to get the same input as the one used in cBioPortal to calculate Z-scores (data_mrna_seq_v2_rsem.txt). The transformation method isn't in the documentation and I also have read RSEM's article, but haven't found any explanation.

I have read in forums that it consists of dividing all "raw_count" values by the 75th percentile of the column (after removing zeros) and multiplying that by 1000. I have transformed my data using this method but i get much lower values than the ones in cBioPortal, apart form the fact that cBioPortal's file contains negative values, which cannot appear using this percentile transformation.

Regarding TCGA-PRAD study: is this the transformation being applied to raw data? Are there other transformations applied? cBioPortal uses unstranded (raw data) or tpm_unstranded data of RNA-seq? Thank you so much!

Kind regards,

Marina

[de Bruijn, Ino]

Hi Marina,

 

Thanks for reaching out!

 

Unfortunately I’m not very familiar with the RSEM processing. On the cBioPortal side we don’t do any RSEM processing ourselves as far as I know. There’s only z-score calculations

 

Looping in @Madupuri, Ramyasree who might be more familiar with where the RNASeq RSEM data for TCGA Pancan comes from and the transformations we apply

 

Best wishes,

Ino

 

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[Madupuri, Ramyasree]

Hi Marina,

The RSEM data for TCGA Pancer datasets in the portal is from the Pancancer Atlas Publication directly - https://gdc.cancer.gov/about-data/publications/pancanatlas. No additional processing was done by us. 

The raw expression data was normalized and batch corrected to address platform differences, with additional adjustments for sequencing centers etc. For detailed data processing information you can refer to the  'RNA Data Batch Correction' section in the Pancan paper: https://pubmed.ncbi.nlm.nih.gov/29625048/.

Hope this helps!

Thanks,

Ramya

---

From: de Bruijn, Ino <debr...@mskcc.org>
Sent: Tuesday, July 30, 2024 7:03 PM
To: Marina Oteiza <marina...@vhio.net>; cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Cc: Madupuri, Ramyasree <madu...@mskcc.org>
Subject: Re: [EXTERNAL] [cbioportal] RNA-seq raw data transformation

 

[Marina Oteiza]

Hello,

Thank you for your responses. The information and resources provided have been really helpful.

Thanks again for your support!

Kind regards,
Marina