[BioC] Log2 fold change single replicate RNA seq

[john herbert]

I have microarray data, which is 2 colour agilent human of 3 technical
replicates.
Green dye case and Red dye control. I have analysed in Limma,
normalising within arrays and between arrays using aQuantile
normalisation.
I also have some Next gen RNAseq data that has been mapped to the
Refseq transcriptome and I have these raw counts.
However there are no replicates; only one case and one control.
I want to plot how the Log2 Fold change is correlated between the two
data sets as they are looking at similar samples.
The microarray data is easy as Limma reports log2 fold change but NGS
on the other hand does not.
What would be the best package/approach to generating a log2 fold
change of the next gen counts?
I am thinking they should be quantile normalised as the microarray data is????