Hi,

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)

neqc and rma produce log2 values (the help pages tell you this) so you need 2^E to unlog.