Microarray data analysis A practical example using GEPAS

The GEPAS website

Tools roadmap

Data exploration (input) Go to Tools  Viewers  Raw data viewer Select the data from your computer Check desired options, Name your job and Press “Run”. The data will be first loaded and then processed. Wait until you see a green label (with the job name) in the upper right corner of the window.

Data exploration (output-I)

Data exploration (output-II)

Go to Tools --> Normalization --> Affymetrix Select your data (.CEL files compressed in a.zip or.gz file) –If you have already uploaded your data press "select files from the server" –If you haven't uploaded your data yet press "select files from your computer" Leave default options –background correction-rma –normalization - quantiles –PMcorrection - pmonly –summarization -median polish Give the job a name, such as Kidney - Normalization and press "run" Data Normalization (I)

Data Normalization form (input)

Data Normalization output (I)

Data Normalization output (II)