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We can change the plot properties to better visualize the effects of different variables.

Select (Image Added) to open the ConfigurePlot Properties dialog
Set Shape to 4. Batch
Set Size to 3. Time
Set Connect to 5. Treatment Combination
Select OK (Figure 2)

Numbered figure captions

SubtitleText	Configuring plot properties to color by treatment, shape by batch, size by time, and connect by treatment combination
AnchorName	Configure Plot Properties

Image Added

The PCA scatter plot now shows information about treament, batch, and time for each sample (Figure 3).

Numbered figure captions

SubtitleText	PCA scatter plot showing treatment, batch, and time information for each sample. A batch effect is clearly visible.
AnchorName	Configured PCA scatter plot

Image Added

PCA is particularly useful for identifying outliers and batch effects in data sets. We can see a significant batch effect in this dataset as samples cluster by batch. To make this more clear, we can add an ellipses by Batch.

Select (Image Added) to open the ConfigurePlot Properties dialog
Select Ellipsoids from the tab
Select Add Ellipse/Ellipsoid
Select Ellipse
Select Batch from the Categorical Vairable(s) panel and move it to the Group Variable(s) panel
Select OK
Select OK to close the dialog

The ellipses help illustrate that the data is spearated by batches (Figure 4).

Numbered figure captions

SubtitleText	Ellipses around batch groups show that samples separate by batch
AnchorName	PCA plot with ellipses

Image Added

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