Protocols for running common analyses in GenePattern

Run an Analysis in GenePattern
Learn how to run an analysis in GenePattern by preprocessing gene expression data and visualizing the resulting data as a heat map.

Differential Expression Analysis
Find genes that are significantly differentially expressed between classes of samples.

Clustering
Group genes and/or samples by similar expression profiles.

Prediction
Create a model, also referred to as a classifier or class predictor, that correctly classifies unlabeled samples into known classes.

SNP Copy Number and Loss of Heterozygosity Determination
Compute SNP copy number (CN) and loss of heterozygosity (LOH) based on Affymetrix SNP chip data for paired target/normal samples.