A method of normalizing a nucleic acid library comprising target nucleic acids, comprising: (a) obtaining a substrate having a normalizing amount of capture probes attached thereto, wherein the capture probes comprise first amplification sites; (b) hybridizing a plurality of target nucleic acids to the capture probes; (c) extending the capture probes to obtain extended probes, wherein the extended probes comprise second amplification sites; and (d) amplifying the extended probes by hybridizing extension primers to the second amplification sites, wherein the amount of the extension primers is equal to or greater than the normalizing amount of capture probes, wherein the amplification is performed such that substantially all the capture probes are extended, thereby obtaining a normalizing amount of amplified target nucleic acids; wherein the first amplification sites and the extension primers are incapable of or are essentially incapable of hybridizing to one another; and wherein: (i) the first amplification sites and the extension primers each lack the same type of nucleotide, or (ii) the first amplification sites lack types of nucleotides complementary to one another, and each extension primer consists essentially of the same types of nucleotides as the first amplification site, or (iii) the first amplification sites lack at least one type of nucleotide selected from adenine (A), cytosine (C), guanine (G), and thymine (T), and optionally, wherein the first amplification sites lack a combination of nucleotides selected from: adenine (A) and thymine (T); or guanine (G) and cytosine (C). (a) obtaining a substrate having a normalizing amount of capture probes attached thereto, wherein the capture probes comprise first amplification sites; (b) hybridizing a plurality of target nucleic acids to the capture probes; (c) extending the capture probes to obtain extended probes, wherein the extended probes comprise second amplification sites; and (d) amplifying the extended probes by hybridizing extension primers to the second amplification sites, wherein the amount of the extension primers is equal to or greater than the normalizing amount of capture probes, wherein the amplification is performed such that substantially all the capture probes are extended, thereby obtaining a normalizing amount of amplified target nucleic acids; wherein the first amplification sites and the extension primers are incapable of or are essentially incapable of hybridizing to one another; and wherein: (i) the first amplification sites and the extension primers each lack the same type of nucleotide, or (ii) the first amplification sites lack types of nucleotides complementary to one another, and each extension primer consists essentially of the same types of nucleotides as the first amplification site, or (iii) the first amplification sites lack at least one type of nucleotide selected from adenine (A), cytosine (C), guanine (G), and thymine (T), and optionally, wherein the first amplification sites lack a combination of nucleotides selected from: adenine (A) and thymine (T); or guanine (G) and cytosine (C). (i) the first amplification sites and the extension primers each lack the same type of nucleotide, or (ii) the first amplification sites lack types of nucleotides complementary to one another, and each extension primer consists essentially of the same types of nucleotides as the first amplification site, or (iii) the first amplification sites lack at least one type of nucleotide selected from adenine (A), cytosine (C), guanine (G), and thymine (T), and optionally, wherein the first amplification sites lack a combination of nucleotides selected from: adenine (A) and thymine (T); or guanine (G) and cytosine (C). <EOS>