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????

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