data extraction cdna arrays affy arrays. stanford microarray database

Data Extraction

cDNA arrays

Affy arrays

Stanford microarray database

Go into public login select organism and the author

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

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

Display data for each slide and download

Or you can chose to data retrieval

Click on data analysis to select experiments to download

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

Proceed to data filtering

Retrieve data

Download preclustering file: unnormlalized data

Save unnormalize data as text file

Open data file in excel

Proceed to gene filtering

Click on filter data and download median normalized data

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

Affymetrix Data: Go to GEO

Type in a keyword and select a study

Experimental Series Information

Pubmed

Individual array information

Individual array information

Some have .cel files available as suplementary materials

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

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

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

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

Normalization Methods for raw data

Double channel cDNA (channel intensities)

Affymetrix oligo arrays (.cel files)