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Genomics Suite Documentation

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Table of Contents
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Scatter Plot

A scatter plot is a simple way to visualize differentially expressed genes. We can plot a scatter plot with gene expression values for two samples at one time. While most probe(sets)/genes fall on a 45° line, up- or down-regulated genes are positioned above or below the line.

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

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

MA Plot

The MA plot can be used to disaply a different in expression patters 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 to the side so that the differentially epxressed 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 values follow a horizontal line. 

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