How do I compare gene expression between subgroups?

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This page assumes you have a column on screen that has the groups you would like to compare (such as 'sample type' for comparing tumor vs normal') or have already made subgroups (such as 'has mutations in EGFR'). If you need help making subgroups, please go to the 'How do I make subgroups' help page.
First, make sure that the gene or genes that you want to use in the comparison are on screen. Click on the charts icon in the top right  and choose 'Compare subgroups'. Click the dropdown for 'Show data from' and choose you gene expression column. Click the dropdown for 'Subgroup samples by' and choose your subgroup column. Choose if you would like a box plot or violin plot and click 'Done'. 
Example
Below we examine patient's samples that have aberrations in EGFR  in the TCGA Lung Adenocarcinoma study. We will investigate if patient's samples that have aberrations in EGFR (mutations or copy number amplifications) have higher expression.
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https://xenabrowser.net/?bookmark=d31da9334a490d3cc5b5b75446e679a1
Steps
1.
Click the graph icon in the upper right corner to enter Chart View.
2.
Click 'Compare subgroups', since we want to compare the group of samples who have aberrations in EGFR to the group of samples that do not.
3.
Click the dropdown for 'Show data from' and choose 'column C: EGFR - gene expression RNAseq - HTSeq - FPKM-UQ'.
4.
Click the dropdown for 'Subgroup samples by' and choose 'column B: (mis OR infra) OR C:>0.5 - Subgroup'.
5.
Click 'Done'. 
Video of steps
For more information see our Basic Tutorial: Section 3, where this example was pulled from.

How do I make more than 2 subgroups?

How do I make subgroups with geneA high and geneB high?

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Contents

Example

Example

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Steps

Video of steps

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