Comparison of GenomeStudio v2.0 and GenomeStudio v2011.1

GenomeStudio software is used for the analysis of Illumina Infinium array data and is available in two distinct versions. This article describes the key differences between GenomeStudio v2.0 and GenomeStudio v2011.1, and provides guidance on selecting the most appropriate version based on the intended analysis workflow and data requirements.

Refer to the table below to determine the recommended GenomeStudio software version for specific array analysis.

Table 1. Comparison of GenomeStudio v2.0 and GenomeStudio v2011.1, highlighting key features and functional differences.

Feature	GenomeStudio v2.0	GenomeStudio v2011.1
Supported Array Type	Genotyping and Cytogenetics	Genotyping, Cytogenetics and Methylation
Available Modules	Genotyping	Genotyping*
Polyploid Genotyping	Methylation
	Gene Expression**
GenTrain Version	3.0	2.0

* The Genotyping Module in GenomeStudio v2011.1 uses the legacy GenTrain 2.0 algorithm and does not support GenTrain 3.0. Consequently, cluster files generated in GenomeStudio v2.0 are not compatible and cannot be used to create projects in GenomeStudio v2011.1.

** Illumina no longer manufactures Gene Expression BeadChips.

Notes:

• Only GenomeStudio v2011.1 can be used to create Methylation projects. For genotyping projects, GenomeStudio v2.0 is recommended.

• License keys for GenomeStudio v2011.1 are provided in the GenomeStudio v2011.1 license keys.txt file included with the installer. For additional assistance with installation, refer to the article Where to find required license keys / serial numbers for installation of GenomeStudio v2011.1.

• Both versions are installable in the same computer without mutual interference, as long as the computer meets the GenomeStudio computing requirements.

For any feedback or questions regarding this article (Illumina Knowledge Article #2887), contact Illumina Technical Support [e-mail].