Frequently Asked Questions
Yes, you can run correlation analysis on the entities of your interest in GeneSpring 13.0. Select “Correlation” from the “Analysis” section in the workflow browser and select the entity list of interest in the Correlation Analysis window.
Correlation analysis in quality control on samples operates on all entities and all samples and is calculated using Pearson correlation. However, correlation under analysis allows you to perform sample level correlation on the entity list of your interest. You could also limit the correlation calculation on a specific set of samples as defined in an interpretation. In addition to Pearson similarity, GeneSpring also provides you with the Spearman method of correlation co-efficient calculation.
Yes, you can perform correlation analysis on a combination of up to two omics types. Create an MOA experiment with the two corresponding experiments. Please note: the two experiments have to be in the same project to be able to create an MOA experiment.
Yes, it is possible to filter the displayed entities based on list associated values, like fold change or regulation, using the “Show filters” icon. The icon can be found on the extreme left of the correlation heatmap view toolbar. Select “Up” from the regulation tab to limit the view to up-regulated entities.
Yes, you can display the section representing correlation across experiments using the “Show across experiment correlation view” icon. This is the first icon from the right in the correlation heatmap view toolbar.
GeneSpring uses correlation coefficient values to build the correlation clustered heatmap.
Correlation coefficient values can be exported through Right-click on the Heatmap -> Export correlation coefficients. You can choose to export either all the correlation values, values for a filtered list or only highlighted entities.