Composite arrays utilizing microspheres

1. A method of making a composite array composition comprising:

a) providing a substrate with a surface comprising a plurality of assay locations, each assay location comprising an array location, said array location comprising a plurality of discrete sites; and

b) providing a population of microspheres comprising at least a first and a second subpopulation, wherein said first subpopulation comprises a first bioactive agent and wherein said second subpopulation comprises a second bioactive agent;

wherein said microspheres are randomly distributed in said discrete sites in said array location; and

c) contacting said randomly distributed microspheres with a plurality of different decoder binding ligands, whereby the location of said bioactive agents is determined.

2. A method of making a composite array composition comprising:

a) randomly distributing a population of microspheres on a substrate with a surface comprising a penalty of assay locations, each assay location comprising an array location, said array location comprising a plurality of discrete sites, wherein said population comprises a first subpopulation of microspheres comprising a first bioactive agent and a second subpopulation of microspheres comprising a second bioactive agent; and

a) following said distributing, contacting said microspheres with a plurality of different decoder binding ligands, whereby the location of said bioactive agents is identified.

3. A method of making a composite array composition comprising:

b) providing a composite array comprising:

i) a substrate with a surface comprising a plurality of assay location, each assay location comprising an array location, said array location comprising a plurality of discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation, wherein said first subpopulation comprises a first bioactive agent and wherein said second subpopulation comprises a second bioactive agent, wherein said microspheres are randomly distributed in said discrete sites in said array location; and

b) following said providing contacting said microspheres with a plurality of different decoder binding ligands, whereby the location of said bioactive agents is identified.

4. A method according to claim 1 , 2 or 3 , wherein each of said assay locations comprises a substantially similar set of bioactive agents.

5. A method according to claim 1 , 2 or 3 , wherein said substrate is a microtiter plate and each assay location is a microtiter well.

6. A method according to claim 1 , 2 or 3 , wherein each discrete site is a bead well.

7. A method according to claim 1 , 2 or 3 , wherein each of said subpopulations further comprise an identifier binding ligand that will bind a decoder binding ligand for identification of said bioactive agent.

8. The method according to claim 7 , wherein said identifier binding ligands are nucleic acids.

9. A method according to claim 8 , wherein said decoder binding ligands are nucleic acid and hybridize with said identifier binding ligands.

10. A method according to claim 1 , 2 or 3 , wherein at least one of said bioactive agents comprises a nucleic acid.

11. A method according to claim 10 , wherein all of said bioactive agents comprise nucleic acids.

12. A method according to claim 11 , wherein at least one of said nucleic acids is a nucleic acid analog.

13. The method according to claim 11 , whereby said decoder binding ligands are nucleic acids and hybridize with said bioactive agents.

14. A method according to claim 1 , 2 or 3 , wherein at least one of said bioactive agents comprises a protein.

15. A method according to claim 1 , 2 or 3 , wherein each of said assay locations comprises at least 1000 discrete sites per cm 2 .

16. A method according to claim 1 , 2 or 3 , wherein each of said assay locations comprises at least 1,000,000 sites/cm 2 .

17. A method according to claim 1 , 2 or 3 , wherein each of said assay locations comprises at least 100 discrete sites.

18. A method according to claim 17 , wherein each of said assay locations comprises at least 500 discrete sites.

19. A method according to claim 18 , wherein each of said assay locations comprises at least 10,000 discrete sites.

20. The method according to claim 1 , 2 or 3 , wherein contacting comprises contacting said microspheres with a pool comprising said plurality of different decoder binding ligands.

21. The method according to claim 20 , wherein said decoder binding ligands are nucleic acids.