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Data Extraction

Learn how to access, retrieve, filter, and analyze microarray data using cDNA arrays and Affy arrays from Stanford's database. Download raw data or preclustered files for further processing. Explore different normalization methods like MAS5, dchip, and rma for accurate analysis.

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Data Extraction

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  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

  5. 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

  23. 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)

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