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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, 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).

Genomics Suite Documentation > Import gene expression data > GX path.png

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

Genomics Suite Documentation > Import gene expression data > gx dialog.png

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.