The following (open access(!)) papers should be relevant:
First, RNA-Seq and DGE are not the same. The protocols differs, and it seems that Illumina has stopped to provide the kit for this technic. RNA-Seq provides a better resolution. Thanks to this you can capture seperatly each transcripts. But you need to be carefull of your coverage. The Mircroarrays are less resolutive and depends of the design of the arrays. And finally the big difference is the cost. And even if you do RNA-Seq you have to make replicates.