cBioportal RNA-seq analysis

[Brewer, Takae]

Hi,

I would like to know what RNA-seq pipeline you used in cBioportal.

Most importantly, would you please tell me how batch effects in TCGA dataset were identified and corrected?

Thank you so much and I look forward to hearing from you.

TMB 

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[Nikolaus Schultz]

Hi,

This manuscript probably has the best description of the batch correction applied to the TCGA PanCancer Atlas RNA expression data:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5957518/

See the Method section called "RNA Data Batch Correction”.

Niki.

On Jan 19, 2022, at 9:33 PM, Brewer, Takae <BREW...@ccf.org> wrote:

Hi,

I would like to know what RNA-seq pipeline you used in cBioportal.

Most importantly, would you please tell me how batch effects in TCGA dataset were identified and corrected?

Thank you so much and I look forward to hearing from you.

TMB 

Please consider the environment before printing this e-mail

Cleveland Clinic is currently ranked as one of the nation’s top hospitals by U.S. News & World Report (2021-2022). Visit us online at http://www.clevelandclinic.orgfor a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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