Question about dataset: Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)

[Zhu, Lihua (Julie)]

Hi,

I have a couple of questions regarding Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016).

 

The summary page states that It contains 2509 samples (http://www.cbioportal.org/study?id=brca_metabric#summary). However, the data_expression.txt file only contains 1906 samples although the data_clinical_sample.txt file does contain 2509 samples. Could you please let me know where to download the mRNA expression values for all 2509 samples? Thanks!

 

In addition, could you please let me know whether the mRNA expression values downloaded from http://www.cbioportal.org/study?id=brca_metabric#summary has been log2 transformed? Thanks!

 

Best regards,

 

Julie

 

 

Lihua Julie Zhu, Ph.D.

Professor

Molecular, Cell and Cancer Biology (MCCB)

Head of Bioinformatics Core, MCCB

Program in Bioinformatics and Integrative Biology

Program in Molecular Medicine

University of Massachusetts Medical School

364 Plantation Street

Worcester, MA

 

[Pichai Raman]

Hello Julie,

A brief review of the paper seems to indicate that they only generated expression data for ~ 2000 samples. So, I don't believe that there is any more expression data but the raw data seems to be here (https://www.ebi.ac.uk/ega/studies/EGAS00000000083). 

And yes the data is log transformed. 

Cheers,

Pichai

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[Zhu, Lihua (Julie)]

Pichai,

Thank you very much for the helpful answer! 

Best regards,

Julie