There are some functions of my code that could not be run using NChannelSet (i.e, Biobase::exprs(raw_data) ). I was just curious if exists some way to transform a NChannelSet object to an expressionSet.
NChannel objects are almost always two-color microarrays. There is more information in the two-channels than in any single expression summary, so any attempt to convert to an expressionSet will lose information. Two-color microarrays are analysed in terms of log-ratios (also called M-values), so the least bad way convert an NChannel object to an expressionSet is to compute the normalized M-values and to use those as the expression matrix. Simply extracting one channel and ignoring the other will give much noisier and possibly meaningless results.