Heatmap Pane

The heatmap pane is a composite of several objects, as seen below. 


heatmap
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Main Heatmap

The heatmap is a grid of cells.   Each column corresponds to one probe.  Each row corresponds to one sample.  The cell is colored by the fold-change of the probe in this sample relative to the average of all samples.  The level in a particular sample is based on an average of all the particles in the sample, as described under statistics.   The value is potentially blank-subtracted, negative-subtracted and normalized, as described under data processing.   The color scale bar at the upper right shows the fold change.

Hovering over a rectangle brings up detailed information for the sample/probe combination.  The arithmetic and logarithmic values are presented.  Also the data values from raw through blank subtraction through negative subtraction through normalization are shown.

Probe Names

The probe names are listed along the top of the axis.   If there are too many names, some names will disappear to allow the remaining names to be displayed.

Probe Tree

The probes are clustered as described under clustering.  Probes that have similar expression levels to each other are placed closed to each other.   The shorter the branches, and the fewer the branches, joining two probes, the closer they are to each other in expression pattern across samples.

Sample Names

The sample names are listed along the top of the axis.   If there are too many names, some names will disappear to allow the remaining names to be displayed.

Sample Tree

The samples are clustered as described under clustering.  Samples that show similar probe expression patterns are placed close together.  The shorter the branches, and the fewer the branches, joining two samples, the closer they are to each other in expression pattern.   Replicates will generally cluster closely together.

Color Scale

The color scale is scaled so the darkest color corresponds to the lowest numerical value in the array, and the brightest color corresponds to the highest numerical value in the array.   Average-expression numbers are white.  The numerical scale is plotted along the color scale for reference.   A negative sample will appear as a dark horizontal bar.  A blank probe will appears as a dark vertical bar.

Variables

The different variables that have been defined appear.   They are also colored according to their values.   For real-valued variables, such as the sample quality ("qc"), the colors run from the lowest to highest value of the variable.   For discrete variables, such as patient gender, or group ID, the color corresponds to the alphabetical order of the group name.

Graph Control Form

Probe Axis Control Form

Sample Axis Control Form



See Also

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