I want to intergrate the mRNA expression data from MRTABRIC and TCGA-BRCA. But METABRIC dataset use micro array to technology to measure mRNA expression, while the TCGA use the RNA-seq methods. So apparently I need to normalize these two data.
Recently I searched an article that the autor have done the same data process. But I am quite confussing about their Supplementary method, which described as :
Metabric: Each gene was scaled so that the 2.5% and 97.5% quantiles equalled -1 and +1, respectively.
TCGA: A voom normalization was applied on the raw count using the R package ‘limm'a’ and each gene was scaled so that the 2.5% and 97.5% quantiles equalled -1 and +1, respectively.
I want to ask how to How to implement the method mentioned above. Is there any R packages to do that?
Ref: Bareche, Y et al. “Unravelling triple-negative breast cancer molecular heterogeneity using an integrative multiomic analysis.”
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