Microarray data analysis

A practical example using GEPAS

The GEPAS website

http://gepas.bioinfo.cipf.es/

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)