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With the probe intensities spreadsheet and the gene list open in the Analysis tab, follow these steps to filter the probe intensities spreadsheet. 

• Select the probe intensities spreadsheet in the spreadsheet tree; here, it is Down_Syndrome-GE
• Select Filter from the main task bar
• Select Filter Columns
• Select Filter Columns Base on a List... (Figure 1)

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Now we have a probe intensities spreadsheet containing only the probe intensity values for our 23 genes of interest (Figure 4).

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A Violin Plot tab will open (Figure 5). This plot shows the intensity value ranges of the 23 genes (probe sets) for all samples as violin plots.

• Select View from the main taskbar
• Select Toggle Properties

We can now see the plot properties panel to the left of the violin plot (Figure 6). 

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To improve our view of the gene symbols, we can modify the X-axis legend. 

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Plots can also be split by categorical variables. We can use this to visualize differential expression of genes between Down syndrom and normal patients in different tissue types. 

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There should now be a sub-plot for each category, in this case there are four sub-plots, one for each tissue (Figure 13). There are no error bars for several plots because there are not enough samples in those categories. 

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