How to highlight selected genes in a scatter plot in Array Studio

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Contents

Overview

It is possible to highlight a list of selected genes in an expression scatter plot in Array Studio. One way is to simply use the marquee to select genes of interest, which will be highlighted by default.

Another way is to add a factor column in the annotation table, where genes that should be highlighted should have a distinct factor level (e.g. "yes"). The column can be then used to set color by category in Change Symbol Property.

Steps

Here are the steps of for adding a column “set” using a 9 gene list called “test” to an annotation table and highlighting “test” genes in an expression scatter plot.

Step 1: Create a gene list

Create a List, called "test", containing GeneIDs of interest.

List1.png

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Step 2: Filter for Genes of interest

Apply the list as a filter to GeneID in the Variable tab of the View Controller

ListFilter1.png

3. Select the filter

4. Click the annotation table, click Selection -> Select All Rows

5. Click Selection -> Generate Column from Selection to create a "set" column, in the annotation table of your dataset

AnnotationTable1.png

6. Disselect the list filter in GeneID

7. Select the scatter plot, and set Color by Categorical = “set” in Symbol Properties in Task tab in View Controller

SetColor1.png

ScatterPlot1.png