query

[Kai Chen, SYSU.]

Dear 

I have a question. 

I recently downloaded the METABRIC data for analysis(Breast Cancer (METABRIC, Nature 2012 & Nat Commun 2016)). I am interested in the mRNA expression data. There were two types of the mRNA expression data. One is the Z-score, which is a version after normalization. The other is the Expression log intensity levels (Illumina Human v3 microarray). I would like to consult that for the “Expression log intensity levels” data, did they have ever been normalized? 

Thank you . Kai Chen. 

_______________________________

Kai Chen. M.D.

Dept of Breast surgery,
Breast Tumor Center;  
Sun Yat-sen Memorial Hospital
Sun Yat-sen University, Yingfeng Road No. 33, 510260,
HaiZhu district, Guangzhou, Guangdong,P.R.China
Mobile: 0086-15920164730
Office:0086-020-34071156
Fax:0086-020-34071156
Alternative Email: ckai...@126.com

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[Paul van Dijk]

Hi Ritika,

Regarding the question below (METABRIC expression data normalized or not?):

I see you performed some curation steps on METABRIC in the past. From https://www.ebi.ac.uk/ega/studies/EGAS00000000083 it looks like data have been normalized. Can you shine a light on this?

Tx!

Paul

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[Paul van Dijk]

Hi Ritika, (or JJ) 

Could you please pay attention to the question by Kai Chen.

Tx

[Paul van Dijk]

Hi Ritika and JJ,

I was just checking whether threads/questions can be marked as completed. This one has not been answered yet. Would be nice if you could still address this question.

Tx

Paul 

[JJ Gao]

Hi Kai,

Sorry for the delay in answering your questions. I am cc'ing the author of METABRIC.

Oscar, would you be so kind as to help answer Kai's question below?

Thanks,

-JJ

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[Oscar Rueda]

Dear Kai Chen, 

Thanks for your interest in METABRIC data. Yes, log intensities have been normalised using specific methods for Illumina arrays (see Curtis et al, Nature 2013) for details. In a nutshell, we did quantile normalisation and probe re-annotation. Let me know if you have any other questions.

Best, 

Oscar M Rueda