# Import gene expression data

This user guide describes how to export gene expression data using Partek's Report Plug-in for Illumina GenomeStudio Gene Expression Module for use in Partek Genome Suite. The GenomeStudio plug-in lets you export data into a project that can be directly opened in Partek Genomics Suite. It is the fastest and most consistent way to get fully annotated Illumina gene expression data into Partek Genomics Suite.

## Partek Gene Expression plug-in installation

Download the plug-in zip file

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unzip the file, there is a folder called **PartekReport** which contains two .dll files --**Partek.Common.dll** and **Partek.GeneExpression.GenomeStudio.dll**, move the **PartekReport** folder to

**C:\Program Files (x86)\Illumina\GenomeStudio\Modules\BSGX\ReportPlugins**, if there is no **ReportPlugins** folder in **BSGX** folder, create one, the path and folder names have to be exactly match one described above (Figure 1).

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-b7d44494421a39de49b3a8e90b41be8681634153%2FGX%20path.png?alt=media)

Figure 1. Place PartekReport folder in the appropriate direcotry

## Export report from GenomeStudio

In GenomeStudio gene expression project:

* Choose **Analysis > Reports...** from the main menu
* Select **Custom Report** and choose **Partek Report Plug-in** from the drop-down list
* Specify *AnnotationName*, do NOT include **<>** in the name, you can the same name as the .bgx file you imported the data with, or a unique name to your dataset
* Choose *Type* by clicking on the cell, default is **gene** level
* Leave all the others as default value (Figure 2)
* Specify the report file name, we recommend to put the exported files in their own folder, which allows you to move the folder instead of all the files individually.
* Click **OK**

![](https://1384254481-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FJVEESmJAPppJ3ijFq5aR%2Fuploads%2Fgit-blob-2f2ab0e8a48d95500624b6e55e51e54e5785e9bf%2Fgx%20dialog.png?alt=media)

Figure 2. Configuring the GenomeStudio gene expression report dialog

There are five files exported, including a project file (.ppj), which can be opened directory in Partek Genomic Suite. The project file opens the signal intensities data in a spreadsheet and associates the annotation information to the intensity spreadsheet. All intensities are log2 transformed. If there are negative values in the AVG\_Signal, the data will be shifted to the lowest value one and then log2 transformed.

## Open project in Partek Genomics Suite

To open the report, launch Partek Genomics Suite, choose **File > Open Project**, browse to the .ppj file to open. In the Gene Expression workflow, you can proceed add sample attribute step.

## 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.