Data Analysis of Microarrays Bioconductor.org “affy” package “limma” package.
Data Extraction cDNA arrays Affy arrays. Stanford microarray database.
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Data Extraction cDNA arrays Affy arrays
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Transcript of 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)
