Run an Analysis in GenePattern


Each GenePattern protocol helps you run an analysis by guiding you from one module to the next. In this protocol, you preprocess gene expression data and use a heat map to visualize the results.

Alternative: You can also run GenePattern modules directly, without using the protocols. The Quick Start provides a quick hands-on introduction to running modules directly.

Before you begin

Gene expression data must be in a GCT or RES file.
Example file: all_aml_test.gct.

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file formats

Step 1: PreprocessDataset

Preprocess gene expression data to remove platform noise and genes that have little variation.

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Step 2: HeatMapViewer

Display a heat map of the preprocessed gene expression data.

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