Gene expression profiling from FFPE samples

A method for analysis of expressed RNA from cells of a deparaffinized FFPE (formalin fixed paraffin embedded) sample, said method comprising:

• indirectly labeling expressed RNA extracted from said cells of said deparaffinized FFPE sample, wherein indirectly labeling comprises synthesizing a plurality of first labeled cDNA strands complementary to said expressed RNA and synthesizing second cDNA strands that are complementary to said first cDNA strands, to form labeled nucleic acids;
• and
• detecting said expressed RNA after hybridization of the labeled nucleic acids to an array.