RNA seq data questions

[Patricia Scott]

Hello cBioPortal Team,

Could you please explain the differences between the different categories of RNA seq data: 

RNA_Seq_v2_expression_median, RNA_Seq_v2_mRNA_median_all_sample_Zscores, RNA_Seq_v2_mRNA_median_Zscores.

Also, which type of data is most appropriate for comparing the effect of expression of a single gene on survival?

Thank you,

Pat Scott

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Patricia Scott

Assistant Professor

Department of Biomedical Sciences

University of Minnesota Medical School Duluth

Tel: 218-726-8361

[JJ Gao]

Hi Pat,

Thanks for contacting us. For the three mRNA profiles:

- "RNA_Seq_v2_expression_median": the original data we retrieved from TCGA, which was processed and normalized using RSEM. (please ignore the median part, it was a misnomer that we will fix soon).

- "RNA_Seq_v2_mRNA_median_all_sample_Zscores": zscore transformed data of "RNA_Seq_v2_expression_median" relative to all the data in the same cohort

- "RNA_Seq_v2_mRNA_median_Zscores": zscore transformed data of "RNA_Seq_v2_expression_median" relative to the diploid samples (based on copy number profile) in the same cohort

There is more information in our FAQ: https://www.cbioportal.org/faq#rna

For comparison, the results based on the three types of profiles should be the same since they are just linear transformation, except that the diploid based zscores (the last one) may miss some genes due to missing copy number data.

Best,

-JJ

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