Answers.Body: <p>Take a look at the section <strong>"Finding Differentialy Expressed Feautres (cluster biomarkers)"</strong> of <a href="https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html" rel="nofollow noreferrer">Seurat tutorial</a>.</p>
  
  <p>You have to define your clusters (if not computed automatically) by modifying the <strong><em>ident</em></strong> slot of the Seurat object.</p>
  
  <p>Then you call the function <em>FindMarkers</em> of your Seurat object (to define markers of a given cluster against the rest) or <em>FindAllMarkers</em> (to look for all the combinations) </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-21T07:56:36.830Z
Answers.Text: How can I modify the ident slot based on a gene and not on a cell population ?
Answers.UserDisplayName: Iro Pierides
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Answers.CreationDate: 2019-05-21T08:41:01.860Z
Answers.Text: You should decide which cells express your EYPF marker and then give this information to the ident slot.
Answers.UserDisplayName: jxx_fa
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Answers.CreationDate: 2019-05-21T12:44:24.003Z
Answers.Text: The cells are dispersed all over the tSNE plot and are not within a specific cell cluster. How do I group them together>
Answers.UserDisplayName: Iro Pierides
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Answers.CreationDate: 2019-05-21T13:29:50.203Z
Answers.Text: You can create your own clusters/grouping by expression. For instance, all the cells that express more than 10 molecules of EYPF you assign them to a group and the rest to other. This has nothing to do with the tSNE plot at the end, is a matter of grouping cells by expression of a marker gene. Then you assign the manual clusters that you have created via the ident slot and perform differential expression.
Answers.UserDisplayName: jxx_fa
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-05-21T13:40:31.713Z
Answers.Text: I am new to this and don't know the exact syntax. Could you provide a specific code for defining the ident slot, please? That would be very helpful, thanks
Answers.UserDisplayName: Iro Pierides
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Answers.CreationDate: 2019-05-21T13:53:05.547Z
Answers.Text: I mean I don't know how to group cells based on gene expression
Answers.UserDisplayName: Iro Pierides
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Answers.Text: @plat Hi plat, can you give me the detailed code about assign the manual cluster that I can create via the ident slot and perform differential expression?
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Body: <p>I want to define the identity of some cells based on a gene marker (for example the colour yellow&lt; EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the differential gene expression between those groups that are found on the same cell sample. Do you have any tips for a code in Seurat? Thanks</p>
  
Tags: <seurat>
Title: Differential expression between two types of cells of specific marker gene expression
ThreadText: # Differential expression between two types of cells of specific marker gene expression
  
  (Asked by: username_0 on 2019-05-20)
  
  I want to define the identity of some cells based on a gene marker (for example the colour yellow< EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the differential gene expression between those groups that are found on the same cell sample. Do you have any tips for a code in Seurat? Thanks
  
  **Tags:** seurat
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-05-20. Score: 1
  
  Take a look at the section **"Finding Differentialy Expressed Feautres (cluster biomarkers)"** of [Seurat tutorial](https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html).
  
  You have to define your clusters (if not computed automatically) by modifying the ***ident*** slot of the Seurat object.
  
  Then you call the function *FindMarkers* of your Seurat object (to define markers of a given cluster against the rest) or *FindAllMarkers* (to look for all the combinations)
  
  > **Comments:**
  > **username_0**: How can I modify the ident slot based on a gene and not on a cell population ?  
  > **username_1**: You should decide which cells express your EYPF marker and then give this information to the ident slot.  
  > **username_0**: The cells are dispersed all over the tSNE plot and are not within a specific cell cluster. How do I group them together>  
  > **username_1**: You can create your own clusters/grouping by expression. For instance, all the cells that express more than 10 molecules of EYPF you assign them to a group and the rest to other. This has nothing to do with the tSNE plot at the end, is a matter of grouping cells by expression of a marker gene. Then you assign the manual clusters that you have created via the ident slot and perform differential expression.  
  > **username_0**: I am new to this and don't know the exact syntax. Could you provide a specific code for defining the ident slot, please? That would be very helpful, thanks  
  > **username_0**: I mean I don't know how to group cells based on gene expression  
  > **username_2**: @plat Hi plat, can you give me the detailed code about assign the manual cluster that I can create via the ident slot and perform differential expression?  
  
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