1. Data Extraction cDNA arrays Affy arrays

2. Stanford microarray database

3. Go into public login select organism and the author

4. If you chose to display data, you can access raw data

6. Display data for each slide and download

7. Or you can chose to data retrieval

8. Click on data analysis to select experiments to download

9. Click on data retrieval, use default selections, select gene name, accession etc.

10. Proceed to data filtering

11. Retrieve data

12. Download preclustering file: unnormlalized data

13. Save unnormalize data as text file

14. Open data file in excel

15. Proceed to gene filtering

16. Click on filter data and download median normalized data

17. You may chose to download raw data for channel 1 and channel 2 to do other normalizations

18. Affymetrix Data: Go to GEO

19. Type in a keyword and select a study

20. Experimental Series Information

21. Pubmed

22. Individual array information

24. Some have.cel files available as suplementary materials

25. Other examples of sample files normalized differently: e.g., MAS5

26. Other examples of sample files normalized differently: e.g., dchip

27. Other examples of sample files normalized differently: e.g., rma

28. You can download the normalized or raw (.cel file) data

29. Normalization Methods for raw data Double channel cDNA (channel intensities) Affymetrix oligo arrays (.cel files)