I tried to perform a differential gene expression analysis using Limma for some data that resemble microarray data. They are obtained from nanostring and when I performed the Limma I get logFC values that are in the 100s like -500 etc. I don't know if I am doing something wrong with the data set. I tend to make an ExpressionSet using the normalised counts matrix and metadata.
Should I be trying to convert the normalised counts matrix into log-ratios or log-expression values in which case how would I fo about doing this?