GEO2R

GEO Publications
FAQ
MIAME
Email GEO

NCBI » GEO » GEO2R Login

Warning: This tool requires JavaScript to function. Learn how to enable javascript

Use GEO2R to compare two or more groups of Samples in order to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. Full instructions

Warning: This analysis might not be applicable to series of type ""
GEO accession	Set
Platform

Samples

GEO2R
Value distribution
Options
Profile graph
R script

Quick start

Specify a GEO Series accession and a Platform if prompted.
Click 'Define groups' and enter names for the groups of Samples you plan to compare, e.g., test and control.
Assign Samples to each group. Highlight Sample rows then click the group name to assign those Samples to the group. Use the Sample metadata (title, source and characteristics) columns to help determine which Samples belong to which group.
Click 'Top 250' to perform the calculation with default settings.
Results are presented as a table of genes ordered by significance. The top 250 genes are presented and may be viewed as profile graphs. Alternatively, the complete results table may be saved.
You may change settings in Options tab.

How to use

Log-transformation has been applied to the data. You can change this in the Options tab.

Save all results Show all columns Select columns

Data columns

Adj P-value
P-value
t-statistic
B-value
logFC
F-statistic

Annotation columns

Set Cancel Restore defaults

Calculate the distribution of value data for the Samples you have selected. Distributions may be viewed graphically as a box plot or exported as a number summary table. The plot is useful for determining if value data are median-centered across Samples, and thus suitable for cross-comparison. More...

View

Export

Apply adjustment to the P-values. More...

Benjamini & Hochberg (False discovery rate)
Benjamini & Yekutieli
Bonferroni
Hochberg
Holm
Hommel
None

Apply log transformation to the data. More...

Auto-detect
Yes
No

Category of Platform annotation to display on results.

If you edit Options after performing an analysis, you must click Recalculate on the GEO2R tab to apply the edits.

Enter ID:

Set

This tab allows you to view a specific gene expression profile graph by entering the corresponding identifier from the ID column of the Platform record. This feature does not perform any calculations; it merely displays the expression values of the gene across Samples. Sample groups may or may not be defined for this feature to work.