Answers.Body: <p>There's no default for the <code>export_to</code> option, so you just need to specify <code>export_to="Seurat"</code>. Note that monocle2 doesn't seem to be compatible with the newest Seurat (3.1) releases.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-21T10:23:14.327Z
Answers.Text: It is possible to update Seurat v2 objects to Seurat v3 objects via `UpdateSeuratObject()`.
Answers.UserDisplayName: haci
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Answers.CreationDate: 2020-03-21T10:57:21.390Z
Answers.Text: I don’t know off hand, maybe give it a whirl and see.
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2020-02-20T09:37:27.830Z
Answers.LastActivityDate: 2020-02-20T09:37:27.830Z
Answers.UserDisplayName: Devon Ryan
Body: <p>I have tried to export the monocle data into Seurat and got the error</p>
  
  <pre><code>"Error in Seurat::CreateSeuratObject(raw.data = data, normalization.method = "LogNormalize",  :
    unused arguments (raw.data = data, normalization.method = "LogNormalize", do.scale = TRUE, do.center = TRUE, is.expr = monocle_cds@lowerDetectionLimit)
  Calls: exportCDS
  In addition: Warning message:
  In if (export_to == "Seurat") { :
    the condition has length &gt; 1 and only the first element will be used"
  </code></pre>
  
  <p>Here is my code <code>seurat_SAN_cds_subset &lt;- exportCDS(SAN_cds_subset)</code></p>
  
  <p>Is anyone familiar with this?</p>
  
Tags: <seurat><single-cell><monocle>
Title: how to export the monocle data into Seurat
ThreadText: # how to export the monocle data into Seurat
  
  (Asked by: username_0 on 2019-11-25)
  
  I have tried to export the monocle data into Seurat and got the error
  
  ```
  "Error in Seurat::CreateSeuratObject(raw.data = data, normalization.method = "LogNormalize",  :
    unused arguments (raw.data = data, normalization.method = "LogNormalize", do.scale = TRUE, do.center = TRUE, is.expr = monocle_cds@lowerDetectionLimit)
  Calls: exportCDS
  In addition: Warning message:
  In if (export_to == "Seurat") { :
    the condition has length > 1 and only the first element will be used"
  
  ```
  
  Here is my code `seurat_SAN_cds_subset <- exportCDS(SAN_cds_subset)`
  
  Is anyone familiar with this?
  
  **Tags:** seurat, single-cell, monocle
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-20. Score: 1
  
  There's no default for the `export_to` option, so you just need to specify `export_to="Seurat"`. Note that monocle2 doesn't seem to be compatible with the newest Seurat (3.1) releases.
  
  > **Comments:**
  > **username_2**: It is possible to update Seurat v2 objects to Seurat v3 objects via `UpdateSeuratObject()`.  
  > **username_1**: I don’t know off hand, maybe give it a whirl and see.  
  
  ---
  
  