What is the normalization status of metabric data?
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Entering edit mode
20 months ago
DareDevil ★ 4.3k

I used the data_mrna_agilent_microarray.txt data from the portal brca_metabric. The information about this data are given in the file meta_mrna_agilent_microarray.txt The information is as follows:

cancer_study_identifier: brca_metabric
genetic_alteration_type: MRNA_EXPRESSION
datatype: CONTINUOUS
stable_id: mrna
show_profile_in_analysis_tab: false
profile_name: mRNA expression (microarray)
profile_description: Expression log intensity levels (Illumina Human v3 microarray)
data_filename: data_mrna_agilent_microarray.txt

The information does not tell me whether the data is normalized or not?

metabric normalization microarray cbioportal • 632 views
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Entering edit mode
4 weeks ago
etiennedanis ▴ 20

I just found an answer to this question here:

https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ

"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."

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