I am using
limma for analyzing both Illumina and Affymetrix expression microarray datasets and apply
neqc function for Illumina and
rma for Affymetrix arrays. I am interested in extracting non-logged form of data for downstream analysis however I could extract the normalized log-intensities for both arrays, How do I obtain unlogged normalized values. Which one of the below function seems appropriate for this?
A. no.log.expression <- 2^x$E (OR) B. antilog_data <- exp(x$E)