GenomeStudio FAQs

Yes, GenomeStudio is supported on Windows XP, Vista, and Windows 7.  

New software releases are announced via our Illuminotes e-newletter. You can request the latest versions by emailing the catalog number and your shipping and billing addresses to orders@illumina.com. Software updates are free for customers with a current service contract (warranty). Hot fixes are available for download from our website. You can also contact your Field Applications Scientist or technical support to find out the most recent software versions available.

Unique GenomeStudio Software 2011.1 license keys were discontinued in July 2016. License keys for each of the GenomeStudio 2011.1 modules are included in a text file with the software installer download without charge. See GenomeStudio Software Downloads.

With GenomeStudio software open, go to the Help menu and select About. The About screen includes GenomeStudio software version information.

The table below includes Illumina’s minimum hardware recommendations to run GenomeStudio software.

The diff score is a transformation of the p-value that provides directionality to the p-value based on the difference between the average signal in the reference group and the comparison group.

The formula is: DiffScore = 10*sgn(µcond-µref)*log10p.

• For a p-value of 0.05, DiffScore = ± 13
• For a p-value of 0.01, DiffScore = ± 22
• For a p-value of 0.001, DiffScore = ± 33

The p-value column is hidden by default. To display this column, use the Column Chooser.

Filter the genes using the Detection p-value. Setting detection at .99 (p value <0.01) means that there is a 1% false positive rate.

Yes. See the GenomeStudio downloads for the latest GenomeStudio installer. You can choose to install the GenomeStudio Framework, which does not require a licence key, by selecting the respective box in the install wizard. GenomeStudio Genotyping Module does not need to be installed on the same computer on which the Polyploid Genotyping Module is installed. However, the polyploid workflow does require generating a genotyping project in the GenomeStudio Genotyping Module prior to taking the data to the Polyploid Genotyping Module for polyploidy clustering. 

No, the Polyploid Genotyping module is a standalone software which does not require a license key.

The Polyploid Genotyping Module has the same computing requirements as other GenomeStudio Microarray modules listed in the GenomeStudio computing requirements.

Illumina does not provide recommendations for downstream analysis outside of GenomeStudio.

No, it is not possible to generate a new project in the Polyploid Genotyping Module directly from idats. The polyploid workflow requires to first generate a genotyping project in the GenomeStudio Genotyping Module from the idats. The genotyping project (.bsc) can then be opened in the Polyploid Genotyping Module for polyploidy clustering.

SNPs are only clustered for samples selected in the Samples Table (marked in blue). If no samples are selected in the Samples Table, SNPs are clustered for all samples in the Samples Table (except non-excluded samples). To cluster SNPs for all your non-excluded samples, make sure that no samples are selected in the Samples Table at the time of clustering (eg, by clicking onto an area in the SNP graph).

You can configure the following parameters to manipulate the default clustering algorithms: Minimum Number of Points in a Cluster, Cluster Distance, and Maximum Number of Clusters in the SNP Table, which is in the Clustering Options dialog box.

Cluster distance specifies the maximum distance that samples can be away from each other and still considered part of the same cluster. Increasing cluster distance will result in fewer clusters that are larger in size, while decreasing cluster distance will result in more clusters which are smaller in size. A cluster distance of 0.06 is typically a good starting point for initial clustering.

Data can be exported directly from the Samples Table, SNP Table, and Full Data Table for downstream analysis. Mark the columns and rows you wish to export and click the icon for "Export displayed data to file" to save selected table contents in *.txt or *.csv format.

No, the Polyploid Genotyping Module performs cluster assignment, but does not call genotypes. This is because the assignment of genotypes polyploid species is highly dependent on the population and biology of the organism. Any downstream genotype assignment should be done with the biology and evolutionary history of the population taken into consideration.

No, a polyploid project (.pcm) can only be opened using the Polyploid Genotyping Module.

No, this is not an option in the Polyploid Genotyping Module.

This value must be non-zero. Illumina recommends setting the Minimum Number of Points in Cluster to match the biology of your samples and the size of your data set. The general guideline is to set the value to 1–4% of the number of samples that are performing well in the data set.

There are no restrictions; however we recommend that the Maximum Number of clusters is set to match the biology of your samples.

OPTICS is an acronym for Ordering Points to Identify Clustering Structure. As a subalgorithm of DBSCAN, it was developed to be more robust to changes in input parameters. This trait makes OPTICS more suited for initial clustering.

DBSCAN is an acronym for Density-Based Spatial Clustering of Applications with Noise. This algorithm is more sensitive to initial input parameters, such as cluster distance. It is more suited for differentiating clusters that are very close together, and is typically applied to SNPs for which OPTICS does not yield satisfactory results.

No. New settings are only applied to any SNPs clustered after applying changes.

You can evaluate and sort samples by Poly Call Rate, Poly 10%, and Poly 50%. Illumina recommends using the scatterplot function in the Samples table to plot Poly 50% against Poly Call Rate to graphically visualize sample outliers.

Call Rate is carried over from the Samples Table in the GenomeStudio Genotyping Module in which the original genotyping project (.bsc) was created. Entries in the Call Rate column do not change when SNPs are clustered in the PC Module. In contrast, the Poly Call Rate is calculated from clustering SNPs in the PC Module and represents the percentage of SNPs for which a given sample was assigned to a cluster.

You can evaluate and sort SNPs by Call Freq, # no calls, Poly 10%, and Poly 50%.

The PC Module is compatible with GenomeStudio Genotyping projects created from Infinium and GoldenGate genotyping assays run on the iScan System, HiScan System, BeadXpress Reader, or BeadArray Reader.