if you have very few starting material you can use RNA FISH from affymetrix http://www.affymetrix.com/estore/promotions/qgviewrna/index.affx it is more pricy but the result are great and you can see the heterogeneity of the expression of your gene in function of cellular type. you can do 2-3 mRNA in the same time in fluorescence or color based...
Many perfect kits from life technology and Qiagen are available to extract RNA from FFPE, which can be used for varaiety of down stream procedures like Transcriptome analysis, expression studies.