A method for gene expression profiling comprising: a) providing a plurality of target sequences from a paraffin-embedded sample, wherein each target sequence comprises a first target domain and a second target domain; b) hybridizing each target sequence with a set of ligation probes each comprising: i) a first ligation probe of 12 to 35 nucleobases comprising: 1) a first probe domain complementary to said first target domain; and 2) a 5'-ligation moiety; and ii) a second ligation probe of 12 to 35 nucleobases comprising: 1) a second probe domain complementary to said second target domain; 2) a 3' ligation moiety; wherein said first and second ligation probes are hybridized to said first and second target domains respectively, and wherein at least one of said first and said second ligation probes comprises an anchor sequence; b) providing conditions such that the ligation moieties of each of the first and second ligation probes react, thereby chemically ligating said first and said second ligation probes to form a plurality of ligation products; c) releasing said ligation products from said target sequences; d) capturing said released ligation products on an array comprising a plurality of capture probes each complementary to one of said anchor sequences; and e) detecting the presence of said ligation products. a) providing a plurality of target sequences from a paraffin-embedded sample, wherein each target sequence comprises a first target domain and a second target domain; b) hybridizing each target sequence with a set of ligation probes each comprising: i) a first ligation probe of 12 to 35 nucleobases comprising: 1) a first probe domain complementary to said first target domain; and 2) a 5'-ligation moiety; and ii) a second ligation probe of 12 to 35 nucleobases comprising: 1) a second probe domain complementary to said second target domain; 2) a 3' ligation moiety; wherein said first and second ligation probes are hybridized to said first and second target domains respectively, and wherein at least one of said first and said second ligation probes comprises an anchor sequence; b) providing conditions such that the ligation moieties of each of the first and second ligation probes react, thereby chemically ligating said first and said second ligation probes to form a plurality of ligation products; c) releasing said ligation products from said target sequences; d) capturing said released ligation products on an array comprising a plurality of capture probes each complementary to one of said anchor sequences; and e) detecting the presence of said ligation products. i) a first ligation probe of 12 to 35 nucleobases comprising: 1) a first probe domain complementary to said first target domain; and 2) a 5'-ligation moiety; and 1) a first probe domain complementary to said first target domain; and 2) a 5'-ligation moiety; and ii) a second ligation probe of 12 to 35 nucleobases comprising: 1) a second probe domain complementary to said second target domain; 2) a 3' ligation moiety; 1) a second probe domain complementary to said second target domain; 2) a 3' ligation moiety; b) providing conditions such that the ligation moieties of each of the first and second ligation probes react, thereby chemically ligating said first and said second ligation probes to form a plurality of ligation products; c) releasing said ligation products from said target sequences; d) capturing said released ligation products on an array comprising a plurality of capture probes each complementary to one of said anchor sequences; and e) detecting the presence of said ligation products.