# Gene Expression Analysis with Batch Effects

This tutorial will will illustrate:

* [Importing the data set](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/importing-the-data-set)
* [Adding an annotation link](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/adding-an-annotation-link)
* [Exploring the data set with PCA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/exploring-the-data-set-with-pca)
* [Detect differentially expressed genes with ANOVA](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/detect-differentially-expressed-genes-with-anova)
* [Removing batch effects](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/removing-batch-effects)
* [Creating a gene list using the Venn Diagram](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/creating-a-gene-list-using-the-venn-diagram)
* [Hierarchical clustering using a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/hierarchical-clustering-using-a-gene-list)
* [GO enrichment using a gene list](https://help.connected.illumina.com/partek/partek-genomics-suite/tutorials/gene-expression-analysis-with-batch-effects/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*](http://www.partek.com/support) *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 [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.