Synthetic tag genes

A method of analyzing the expression of one or more genes, said method comprising:

• (a) providing a pool of target nucleic acids comprising RNA transcripts of one or more of said genes, or nucleic acids derived therefrom using said RNA transcripts as templates;
• (b) providing a spike sample comprising RNA transcribed from a Tag gene or Tag nucleic acids derived from said Tag gene RNA using said Tag gene RNA as template;
• (c) hybridizing said pool of target nucleic acids and said spike sample to an array of oligonucleotide probes immobilized on a surface, said array comprising more than 100 different oligonucleotides, at least some of which comprise control probes and at least some of which comprise probes complementary to said Tag gene or said nucleic acid derived from said Tag gene RNA, wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and at least some of said oligonucleotide probes are complementary to said RNA transcripts or said nucleic acids derived therefrom using said RNA transcripts;
• (d) quantifying the hybridization of said nucleic acids to said array, wherein said quantification is proportional to the expression level of said genes;
• and
• (e) quantifying the hybrization of said spike sample to said array.