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Microarray data analysis

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”.

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Microarray data analysis

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  1. Microarray data analysis A practical example using GEPAS

  2. The GEPAS website http://gepas.bioinfo.cipf.es/

  3. Tools roadmap

  4. 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.

  5. Data exploration (output-I)

  6. Data exploration (output-II)

  7. Data Normalization (I) • 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"

  8. Data Normalization form (input)

  9. Data Normalization output (I)

  10. Data Normalization output (II)

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