Q7. How can I export correlation coefficient values?

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.

Q6. What values are considered while running clustering in correlation view?

GeneSpring uses correlation coefficient values to build the correlation clustered heatmap.

Q5. In MOA, is it possible to only display the section of a correlation heatmap that contains correlation values from across experiments in the Detailed View?

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.

Q4. The input entity list I selected for Correlation Analysis is the result of Fold Change analysis. Is it possible to visualize only Up regulated entities in the heatmap?

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.

Q3. I have data from various omics types. Can I find correlation between entities of my interest from data from various experiments?

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.

Q2. How is correlation analysis available in quality control different from correlation on samples under analysis?

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.

Q1. I have an expression experiment. Is it possible to get correlation values for entities?

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.

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