> For the complete documentation index, see [llms.txt](https://helyx.gitbook.io/geneexpression/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://helyx.gitbook.io/geneexpression/gene-expression-omnibus/analyzing-data.md).

# Analyzing Data

![](/files/-MUaj5w8-GtakajjZa0g)

{% hint style="danger" %}
The MOST IMPORTANT thing you must look out for on the Accession Display page is the blue "Analyze with GEO2R" button at the bottom of the page. You are only able to perform the data analysis described in this lesson if the blue button is there. Not every dataset has the blue button. 
{% endhint %}

Now that we have our dataset (<https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164805>), the next step is to analyze the data.

![Sample raw data from dataset GSE137140](/files/-MUajLdlqqxSmgj8_kA5)

Usually, the raw data is a huge file with potentially thousands of rows and columns. It's not easy to work with as a beginner and without using code. Luckily, the awesome "Analyze with GEO2R" button can do the analysis for us!

&#x20;From the accession page, click on the blue Analyze with GEO2R button.&#x20;

![](/files/-M_YCGr7n_5x_fmmmNAW)

You should see the following page.

![](/files/-MUajgasIvr8nUlMRRb6)

This page will allow you to split the samples into an experimental group and a control group (you have to tell the GEO2R program what to compare with what).

{% hint style="danger" %}
ALWAYS define the EXPERIMENTAL/DISEASE/MUTANT group FIRST!!! This is so the system can properly define what is positive expression and negative expression.&#x20;
{% endhint %}

![](/files/-MUak6Akc_Ie1fmn43Jc)

First, click on the Title column bar to automatically alphabetically sort your samples. It makes it easier to group the samples by type.

{% embed url="<https://www.youtube.com/watch?v=ld5y7BrduRA&feature=youtu.be>" %}

This video shows the steps to define sample groups. Sorry for the low resolution.

In order to select more than one sample at once, simply click on one sample, hold the shift button, and click on another sample. All the samples in between will get selected as well.

![](/files/-MUamuOk-wloITzM7baS)

Your screen should look like this. In this example, we are trying to study the differences in gene expression between COVID-19 patients and normal controls.&#x20;

![](/files/-MUamm182dBZtGJwz7eL)

After splitting your data into 2 groups (10 COVID-19 and 5 controls), click the blue Analyze button (you may need to scroll down the screen).

![](/files/-MUanjZHx-8Gp_HgJoFr)

It may take a few minutes but eventually GEO2R will display the results from your analysis.

Go to the next lesson to learn how to interpret these results.


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://helyx.gitbook.io/geneexpression/gene-expression-omnibus/analyzing-data.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.