Q5. What does the height of a Heatstrip indicate?

The height of a Heatstrip represents an entity’s signal/abundance value at the various experimental conditions.

Q4. How can I view raw data for the genes in Pathway?

By default, the Heatstrips displayed in the Pathway Viewer and in the Heatmap table are normalized signal values. To view raw signal values instead, follow these steps:

Q3. Can I get a Profile Plot of my genes of interest in the pathways?

GeneSpring provides an option to view a Profile Plot of your genes of interest in a pathway. To use this feature, select the genes of interest either from the pathway viewer or the Heatmap table and then click on the Launch Profile Plot icon from the Pathway View Toolbar. A continuous (numerical) or non-continuous (categorical) plot is displayed in a new window based on the interpretation selected during the pathway analysis workflow.

Q2. Can I overlay data from an interpretation different from the one I selected in the Single Experiment Analysis or Multi-Omic Analysis workflow?

Yes, you can view data from a different group of conditions by clicking the Choose another Interpretation icon and selecting another interpretation. Please note that this selection and the associated changes in the Pathway Viewer and the Heatmap table are not saved when the pathway list is closed.

Q1. Why are there grey cells in the Heatmap table in the Pathway View?

Grey cells indicate missing values. The Heatmap table in the Pathway View shows lists all the pathway entities of the same type as that of the input experiment. However, data values are only shown for matching entities with the input experiment.

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