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 Genome Genomics Suite open directly. It is the fastest and most consistent way to get fully annotated Illumina gene expression data into Partek Genomics Suite.

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• 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 ddata 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 recoommend recommend to put the exported files in their own folder, which allows you to move thefolder the folder instead of all the files individually.
• Click OK

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SubtitleText Configuring the GenomeStudio gene expression report dialog AnchorName gxdialog

There are 5 five files exported, including a porject project file (.ppj), which can be opened directory in Partek Genomic Suite. The project file opens the singal signal intensities data in a spreadsheet ans associatte and associates the annotation information to the intensity spreadsheet. All intensities are log2 transformed. If there are negative values in the AVG_Signal, The the data will be shifted to  the the lowest value is 1 one and then log2 transformed.

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

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