Gene Expression Analysis with Batch Effects

This tutorial will will illustrate:

• Importing the data set

• Adding an annotation link

• Exploring the data set with PCA

• Detect differentially expressed genes with ANOVA

• Removing batch effects

• Creating a gene list using the Venn Diagram

• Hierarchical clustering using a gene list

• GO enrichment using a gene list

Note: the workflow described below is enabled in Partek Genomics Suite version 7.0 software. Please fill out the form on Our support page to request this version or use the Help > Check for Updates command to check whether you have the latest released version. The screenshots shown within this tutorial may vary across platforms and across different versions of Partek Genomics Suite.

Description of the Data Set

The data for this tutorial is taken from an experiment that examined the effects of four treatment conditions at two time points on estrogen receptor-positive breast cancer cell lines in vitro. Each treatment/time combination has two replicates and there are two control samples for a total of eighteen samples. Gene expression analysis was performed using the Affymetrix GeneChip_®_ Human U95A array. Values are transformed to log base 2 scale by f(x) = log2(x+1).

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