> For the complete documentation index, see [llms.txt](https://help.partek.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.partek.illumina.com/partek-flow/tutorials/bulk-rna-seq/normalizing-counts.md).
# Normalizing counts
Because different samples have different total numbers of reads, it would be misleading to calculate differential expression by comparing read count numbers for genes across samples without normalizing for the total number of reads.
* Click the **Filtered counts** data node
* Click **Normalization and scaling** in the task menu
* Click **Normalization** (Figure 1)
Figure 1. Invoking Normalization task
The Normalization task set up page will open (Figure 2).
Figure 2. Normalization task set up page
Normalization can be performed by samples or by features. By samples is selected by default; this is appropriate for the tutorial data set.
Available normalization methods are listed in the left-hand panel. For more information about these options, please see the [Normalize counts](/partek-flow/tutorials/bulk-rna-seq/normalizing-counts.md) user guide.
For this tutorial, we will use the recommended default normalization settings.
* Select 
This adds the Median ratio normalization method, which is suitable for performing differential expression analysis using DESeq2 (Figure 3).
Figure 3. Select recommended normalization method
* Click **Finish** to perform normalization
A Normalize counts task node and a Normalized counts data node are added to the pipeline (Figure 4)
Figure 4. Normalize counts task node and Normalized counts data node
## Additional Assistance
If you need additional assistance, please visit [our support page](http://www.partek.com/support) to submit a help ticket or find phone numbers for regional support.
---
# 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, and the optional `goal` query parameter:
```
GET https://help.partek.illumina.com/partek-flow/tutorials/bulk-rna-seq/normalizing-counts.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
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.