Hello,

i want to perform a DGE with data coming from a microarray experiment. My data is already normalized and i am looking for a way to feed it into the limma pipeline.

Is there a convenient way to transform my normalized expression dataset into log expression values and an object that is compatible with lmFit command?

If not, do you have suggestions which package might be better suited to perfom a DGE with normalized microarray expression data than limma?

Best J

lmFit?
#lmFit(object, design=NULL, ndups=NULL, spacing=NULL, block=NULL, correlation, weights=NULL,
#      method="ls", ...)
#object 
#A matrix-like data object containing log-ratios or log-expression values for a series of arrays, with rows #corresponding to genes and columns to samples. Any type of data object that can be processed by getEAWP is #acceptable.

loggedData <- log2(<your normalized data goes here>)

Use limma.