If you analyzing FPKM values which are summarized by genes, the quality (sensitivity and accuracy) might not be as good as Agilent microarrays'. But it may have more information and if you make use more of RNA-seq data, I would recommend browsing and analyzing mapped data in BAM files, which is one step prior to the FPKM calculation. The analysis process is still under development, and you cannot extract meanings just by following textbooks.