In the HELIX project we decided to use residuals instead of M values for the methylation analyses. So, how we get the residuals of a basic lineal model?
Libraries and Data First of all we load the libraries we will use in this test:
library( limma ) # We use lmFit to fit the lineal model library( minfi ) # Methylation data is saved as a GenomicRatioSet library( SmartSVA ) # We want to compute the SVA to correct methylation data library( isva ) # " library( Biobase ) # We will sabe the residuals in an ExpressionSet Once the libraries are loaded we proceed to obtain the methylation data:

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