Single sample group formation to reduce GenomeStudio Methylation Module crashing during analysis

This remedy applies mostly to users not interested in using GenomeStudio Methylation Module’s group analysis or differential analysis features, and are only interested in obtaining results from individual samples in GenomeStudio, with an eye to carrying out more complex analyses using alternate software downstream.

When processing a large number of samples through GenomeStudio Methylation Module in a single project, the program will occasionally crash, with an error message relating to insufficient memory, or may freeze and progress no farther.

During project creation, users navigate through two stages of sample addition--first, the user selects the beadchips and individual samples on those beadchips to be added to the project, and second, the user assigns the samples to specific groups, in order to obtain group average statistics. Users can assign samples to a control group and one or several experimental groups for analysis, establishing groups such as diseased vs normal, treated vs untreated, or other types of group arrangements.

By default, if a user does not designate groups in the sample sheet when creating a project, the software will place all samples in a single default group. Alternatively, when manually creating the groups, if a user is not interested in dividing the samples into groups at this time, they will often manually place all samples in a single default group.

An issue arises if the number of samples in the project is large. Group statistics calculations are carried out regardless of whether users assign all samples to a single group or assign them to various smaller groups. If the single group is inordinately large, the program can bog down at this stage, taking hours to days, or even crash at this step.

To alleviate this, the user can assign each sample to a single-sample group. There are two possible methods:

Method 1: If creating groups manually, select all sample on all beadchips, then select the button with three black arrows pointing to the right.

The result will be that every sample will be placed in its own single-sample group.

Method 2: In the sample sheet, copy all the names of the samples from the Sample_Name column and paste it into the Sample_Group column.

This will result in single-sample groups named after the sample name.

By assigning samples to single-sample-groups, the group statistical analyses simplify group calculations, decrease the time required to complete them, and will be much less likely to crash the program.

For any feedback or questions regarding this article (Illumina Knowledge Article #1887), contact Illumina Technical Support [e-mail].