Expression Intensity Probes.Variable

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Gene Expression intensity

Shows the log2 normalized expression for the specified gene, organized by group (e.g. Primary Site).


When visualizing more than one gene, each gene is shown in its own plot.

X-axis shows log2 expression level. Y-axis shows the group.

filter gene expression by meta data

Use the Sample Tab to further filter the data using any associated sample/subject meta data.

Expression filter1.png

After filtering by primary site:

Expression filter2.png

Use Specify Profile (Task tab) to change the grouping.

Use Specify Split Column (Task tab) to change the automatic coloring.

Show Summary Information displays an on-the-fly p-value, indicating if the expression is significantly changed, of selected group (and split column) using Show Summary Information (Task Tab | Customize). This is calculated by an F-test for One-way or Two-way ANOVA (depending on sample grouping).

Probe level Expression intensity

Shows the log2 normalized probe set expression intensity, organized by group.

Probeset expression intensity.png

How gene level expression is calculated from mapped probe level data

To calculate gene-level expression, the linear probeset measurements are averaged.

The expression data shown in visualizations are log2 normalized, as are the exported text values. To compare the gene level data to the linear-scale values,

  1. Calculate 2 to the power of each expression probe values
  2. Calculate the mean of these values
  3. log2 transform the mean of all values

Linear scaled geneexp.png


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