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.

Before you begin

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

learn more:
file formats

Step 1: PreprocessDataset

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

Open module in the GenePattern window.
Open module with example data in the GenePattern window.

Considerations

PreprocessDataset can preprocess the data in one or more ways (in this order):
1. Set threshold and ceiling values. Any value lower/higher than the threshold/ceiling value is reset to the threshold/ceiling value.
2. Convert each expression value to the log base 2 of the value.
3. Remove genes (rows) if a given number of its sample values are less than a given threshold.
4. Remove genes (rows) that do not have a minimum fold change or expression variation.
5. Discretize or normalize the data.
If you did not generate the expression data, check whether preprocessing steps have already been taken before running the PreprocessDataset module.

learn more:
PreprocessDataset

Step 2: HeatMapViewer

Display a heat map of the preprocessed gene expression data.

Considerations

The HeatMapViewer displays gene expression data as a heat map, which makes it easier to see patterns in the numeric data. Gene names are row labels and sample names are column labels.

learn more:
HeatMapViewer