hi, there are a lot of data preprocessing methods in geo microarray data, here listed at least 5 methods,

1    log2 RMA signal values     ，  
2     MAS5.0 signal intensity 
3     GeneSpring (11.5.1) Normalized Signal Intensity，
4     normalized log10 ratio Ch1/Ch2 (test/reference)
5     Normalized signal intensity (Background corrected, log2 transformed, quantile normalized and base line transformed using the median of all samples).

we can see in the geo website, it has geo2r script, all used limma, no matter what happened, just sometimes use log2 when found too huge values, so is it suiatble for limma to do so, especially for data like in GSE55542, there is negtive value after variety ways of preprocess(in fact method 5)

so is it suitable?

limma is routinely used for all the preprocessing methods that you mentioned, and some of them are covered in the limma User's Guide.

Not sure what problem you are worried about. limma has no problem with any of processing methods, whether negative values or not. Intensities can obviously be negative on the log-scale and that doesn't cause any problems. Unlogged intensities can also be negative after background correction, and limma handles that by normexp background correction.