Answers.Body: <p>No Seurat function is needed. In the seurat object &quot;cells&quot;, you can access the raw counts or normalized counts using <code>cells@assays$RNA@counts</code> (raw counts) or <code>cells@assays$SCT@data</code> (SCT normalized data)</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-06-06T22:25:35.370Z
Answers.LastActivityDate: 2022-06-06T22:25:35.370Z
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Body: <p>I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster.</p>
  <p>I've gone ahead and subsetted the cluster of interest.</p>
  <pre><code>tumor &lt;- subset(x = data, idents = c(&quot;Tumor&quot;), invert = FALSE)
  </code></pre>
  <p>How would I calculate the expression values per gene per cell?</p>
  <pre><code>FindAllMarkers
  </code></pre>
  <p>Finds markers (differentially expressed genes) for each of the identity classes in a dataset per ident.</p>
  
Tags: <r><scrnaseq><seurat><gene-expression>
Title: how to calculate the expression values per gene for all cells
ThreadText: # how to calculate the expression values per gene for all cells
  
  (Asked by: username_0 on 2022-06-03)
  
  I'm currently working with a seurat object and I'd like to calculate the expression values per gene for all cells within a particular cluster.
  
  I've gone ahead and subsetted the cluster of interest.
  
  ```
  tumor <- subset(x = data, idents = c("Tumor"), invert = FALSE)
  
  ```
  
  How would I calculate the expression values per gene per cell?
  
  ```
  FindAllMarkers
  
  ```
  
  Finds markers (differentially expressed genes) for each of the identity classes in a dataset per ident.
  
  **Tags:** r, scrnaseq, seurat, gene-expression
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2022-06-06. Score: 2 | Accepted answer
  
  No Seurat function is needed. In the seurat object "cells", you can access the raw counts or normalized counts using `cells@assays$RNA@counts` (raw counts) or `cells@assays$SCT@data` (SCT normalized data)
  
  
  ---
  
  