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  1. Partek Genomics Suite
  2. Tutorials

Gene Expression Analysis with Batch Effects

PreviousAdding gene annotationsNextImporting the data set

Last updated 6 months ago

This tutorial will will illustrate:

Note: the workflow described below is enabled in Partek Genomics Suite version 7.0 software. Please fill out the form on 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).

Additional Assistance

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

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
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