Answers.Body: <p>I don't have enough reputation to comment so I will briefly answer here</p>
  
  <p>This warning is fixed in Seurat 2.3.2. Without upgrading you can ignore this message. It doesn't mean anything for the actual analysis performed so your results won't be flawed.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-13T21:50:08.790Z
Answers.LastActivityDate: 2018-06-13T21:50:08.790Z
Answers.UserDisplayName: Mack123456
Body: <p>I am trying to combine two datasets to be able to compare the cells in them and using <code>Seurat</code> <code>CCA</code> for it:</p>
  
  <p><a href="https://satijalab.org/seurat/Seurat_AlignmentTutorial.html" rel="nofollow noreferrer">https://satijalab.org/seurat/Seurat_AlignmentTutorial.html</a></p>
  
  <p>When I am running <code>AlignSubspace</code> function I am getting a warning for each single dimension that I selected it to be run on:</p>
  
  <pre><code>seurat_union &lt;- AlignSubspace(object = seurat_union, reduction.type = 
      "cca", grouping.var = "protocol", dims.align = 1:13) 
  </code></pre>
  
  <p>So, I am getting 13 warnings:</p>
  
  <pre><code>&gt; warnings()
  Warning messages:
  1: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  2: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  3: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  4: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  5: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  6: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  7: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  8: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  9: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  10: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  11: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  12: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  13: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  </code></pre>
  
  <p>What is this warning telling me? What should I pay attention to with my datasets?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-08T11:02:02.353Z
Comments.Text: Could you please clarify if you had these warnings running the tutorial or with your own dataset? If it is the second case could you please provide information about your data if it is a time series or not, and the type of data you add as an input?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-08T16:45:46.477Z
Comments.Text: With my own dataset. The input is two previously saved Seurat objects. I did analysis of the datasets separately, but then needed to combine them to compare. The input to Seurat objects were raw expression matrices for single cell rna seq data.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-08T17:24:22.677Z
Comments.Text: And are you sure that seurat_union is the type of the object it is needed. It mind if it wouldn't be you would get an error, but a warning might indicate that perhaps you need to add some other type of data with this object or with other attributes. But it simply might be that the dims.align parameter should be something else
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-08T18:22:06.343Z
Comments.Text: I am following the tutorial step by step except that I have already treated the input `Seurat` objects: normalized them, did scaling, clustering, tsne, etc. they way it is specified in a different Seurat tutorial.
Comments.UserDisplayName: Nikita Vlasenko
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-06-08T18:23:41.410Z
Comments.Text: I am able to align them, and work further, it does not give any other error down the line, but I am afraid that something still went wrong, the alignment was not as good as expected and maybe I will get some result at the end but it may be flawed because I did not take into account this warning - that is what I am afraid of
Comments.UserDisplayName: Nikita Vlasenko
Tags: <seurat>
Title: Seurat CCA, AlignSubspace, Argument dist.method is only useful with multivariate timeseries
ThreadText: # Seurat CCA, AlignSubspace, Argument dist.method is only useful with multivariate timeseries
  
  (Asked by: username_0 on 2018-06-08)
  
  I am trying to combine two datasets to be able to compare the cells in them and using `Seurat` `CCA` for it:
  
  <https://satijalab.org/seurat/Seurat_AlignmentTutorial.html>
  
  When I am running `AlignSubspace` function I am getting a warning for each single dimension that I selected it to be run on:
  
  ```
  seurat_union <- AlignSubspace(object = seurat_union, reduction.type = 
      "cca", grouping.var = "protocol", dims.align = 1:13) 
  
  ```
  
  So, I am getting 13 warnings:
  
  ```
  > warnings()
  Warning messages:
  1: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  2: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  3: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  4: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  5: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  6: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  7: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  8: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  9: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  10: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  11: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  12: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  13: In dtw(x = align.1, y = align.2, keep.internals = TRUE,  ... :
  Argument dist.method is only useful with multivariate timeseries
  
  ```
  
  What is this warning telling me? What should I pay attention to with my datasets?
  
  **Tags:** seurat
  
  > **Comments:**
  > **username_1**: Could you please clarify if you had these warnings running the tutorial or with your own dataset? If it is the second case could you please provide information about your data if it is a time series or not, and the type of data you add as an input?  
  > **username_0**: With my own dataset. The input is two previously saved Seurat objects. I did analysis of the datasets separately, but then needed to combine them to compare. The input to Seurat objects were raw expression matrices for single cell rna seq data.  
  > **username_1**: And are you sure that seurat_union is the type of the object it is needed. It mind if it wouldn't be you would get an error, but a warning might indicate that perhaps you need to add some other type of data with this object or with other attributes. But it simply might be that the dims.align parameter should be something else  
  > **username_0**: I am following the tutorial step by step except that I have already treated the input `Seurat` objects: normalized them, did scaling, clustering, tsne, etc. they way it is specified in a different Seurat tutorial.  
  > **username_0**: I am able to align them, and work further, it does not give any other error down the line, but I am afraid that something still went wrong, the alignment was not as good as expected and maybe I will get some result at the end but it may be flawed because I did not take into account this warning - that is what I am afraid of  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2018-06-13. Score: 1 | Accepted answer
  
  I don't have enough reputation to comment so I will briefly answer here
  
  This warning is fixed in Seurat 2.3.2. Without upgrading you can ignore this message. It doesn't mean anything for the actual analysis performed so your results won't be flawed.
  
  
  ---
  
  