Data normalization and processing

[Petar Brlek]

Dear Sir or Madam,

Since I am researching primary brain tumors, your cBioPortal platform is an excellent basis for large-scale analysis of tumor genomics. I am currently using data from two studies from your portal: Brain Lower Grade Glioma (TCGA Firehose Legacy) and Glioblastoma Multiforme (TCGA Firehose Legacy). I would like to kindly ask you, can you give me more detailed and accurate information on how the data on gene methylation, transcription, and protein expression were processed and normalized after the experiment? The question concerns only the data of these two studies of interest (diffuse gliomas). Thank you very much for your help and I hope for a positive response.

Kind regards,
Petar Brlek, MD

[Tali Mazor]

Hi Petar,

In general, we take data as provided by TCGA - the only additional processing we do is to calculate z-scores. You can read about how mRNA data is processed and how z-scores are calculated in our FAQ: https://www.cbioportal.org/faq#rna  As far as I know, we are not normalizing the methylation data in any way. I've cc'ed our lead data curator in case she has anything to add.

You may also want to consider using the TCGA PanCancer Atlas studies rather than the Firehose Legacy - you can read about the differences here: https://www.cbioportal.org/faq#what-are-tcga-firehose-legacy-datasets-and-how-do-they-compare-to-the-publication-associated-datasets-and-the-pancancer-atlas-datasets

-Tali

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