An Illumina-type project file (.bsc format) can be imported in Illumina’s GenomeStudio^® (please note: to process 450K chips, you need GenomeStudio 2010 or newer) and exported using the Partek Methylation Plug-in for GenomeStudio. For more information on the plug-in, please see the plug-in user guide. The plug-in creates six files: a Partek project file (*.ppj), an annotation file (*.annotation.txt), files containing intensity values (*.fmt and *.txt), and files containing β-values (*.fmt and *.txt) (Figure 1). 

To load all the files automatically, open the .ppj file as follows.

• Select Methylation from the Workflows drop-down menu 
• Select Illumina BeadArray Methylation from the Methylation sub-workflows section
• Select Import Illumina Methylation Data from the Import section
• Select Load a project following Illumina GenomeStudio export from the Load Methylation Data dialog