Transcript Molecular Data - Bilkent University

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
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Double channel cDNA (channel
intensities)
Affymetrix oligo arrays (.cel files)