# Perform Exploratory analysis

* [Use Principle Components Analysis (PCA) to reduce dimensions](#use-principle-components-analysis-pca-to-reduce-dimensions)
* [Classify cells based on a marker for expression](#classify-cells-based-on-a-marker-for-expression)

## Use Principle Components Analysis (PCA) to reduce dimensions

* Click the **Normalized counts** data node
* Expand the **Exploratory analysis** section of the task menu
* Click **PCA**

![](/files/IjqeJck3eXJWDUwSGK06)

In this tutorial we will modify the PCA task parameters, to not split by sample, to keep the cells from both samples on the PCA output.

* Uncheck (de-select) the **Split by sample** checkbox under *Grouping*
* Click **Finish**

![](/files/8oDgsyebQ8i7eWdHGSAV)

* Double-click the circular **PCA** node to view the results

![](/files/eU3gio4noRZDKfoAQR0W)

From this PCA node, further exploratory tasks can be performed (e.g. t-SNE, UMAP, and Graph-based clustering).

## Classify cells based on a marker for expression

* Choose **Style** under *Configure*
* **Color by** and search for *fasn* by typing the name
* Select *FASN* from the drop-down

![](/files/kibtFfKnZlW8mAz9Cpuw)

The colors can be customized by selecting the **color palette** then using the color drop-downs as shown below.

![](/files/LknfQr0ull03aOFBIzxf)

Ensure the colors are distinguishable such as in the image above using a blue and green scale for **Maximum** and **Minimum**, respectively.

* Click **FASN** in the legend to make it draggable (pale green background) and continue to drag and drop FASN to **Add criteria** within the **Select & Filter** *Tool*
* Hover over the slider to see the distribution of FASN expression

![](/files/SercMqtv5dYjKeCerE0O)

Multiple gene thresholds can be used in this type of classification by performing this step with multiple markers.

* Drag the slider to select the population of cells expressing high FASN (the cutoff here is 10 or the middle of the distribution).

![](/files/bsy10gWZrqlI7aS5E0we)

* Click **Classify** under *Tools*
* Click **Classify selection**

![](/files/ndqmnPia9e7kibSWXVxa)

* Give the classification a name "FASN high"

![](/files/DEMEdYdJ77Ld71Touwcg)

* Under the Select & Filter tool, choose **Filter** to **exclude** the selected cells

![](/files/SAU4w9ZBeN1tQzB3A2WG)

Exit all Tools and Configure options

* Click the "X" in the right corner
* Use the **rectangle** selection mode on the PCA to select all of the points on the image

![](/files/AwgRldYcytyQzF0m35bP)

This results in 147538 cells selected.

![](/files/fDyk5Xd6SZYl6LMM2d9X)

* Open **Classify**
* Click **Classify selection** and name this population of cells "FASN low"
* Click **Apply classifications** and give the classification a name "FASN expression"

![](/files/Gv4qjSI0erlpXx8vzw44)

Now we will be able to use this classification in downstream applications (e.g. differential analysis).

## 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.


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