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The scatter plot now features a regression line dividing the probe(sets)/genes (Figure 3).

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SubtitleTextEach dot on the plot represents the intensity value of a probe(set)/gene
AnchorNameScatter Plot with Regression Line

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MA Plot

The MA plot can be used to disaply display a different difference in expression patters patterns between two samples. The horizontal axis (A) shows the average intensity while the vertical axis (M) shows the intensity ratio between the two samples for the same data point. In essence, an MA plot is a scatter plot tileted tilted to the side so that the differentially epxressed expressed probe(sets)/genes are located above or below the 0 value of M. An MA plot is also useful to visualize the results of normalization where you would hope to see the median of hte the values follow a horizontal line. 


The MA plot will launch in a new tab showing the first two rows as the comparison (Figure 4).

Numbered figure captions
SubtitleTextMA plot comparing the expression levels between two samples. Each dot on the plot represents a single genomic feature (gene or probe set). The average signal for each genomic feature is shown on the horizontal axis (A), while the ratio is shown on the vertical axis (M).
AnchorNameMA Plot

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 The samples displayed can be changed using the select sample menus on the left-hand side. 


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