Answers.Body: <p>I was using <code>dudi_pca</code> incorrectly. The supplied parameter to <code>as.matrix()</code> should have been <code>dudi_pca$li</code>:</p>
  
  <pre><code>rtsne_out &lt;- Rtsne(as.matrix(dudi_pca$li), pca=FALSE)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-22T18:29:40.477Z
Answers.LastActivityDate: 2018-01-22T18:29:40.477Z
Answers.UserDisplayName: Nikita Vlasenko
Body: <p>I am trying to run <a href="https://cran.r-project.org/web/packages/Rtsne/Rtsne.pdf" rel="nofollow noreferrer">{Rtsne}</a>. On <code>pca</code> dataset prepared by using <code>dudi.pca</code> from <a href="https://pbil.univ-lyon1.fr/ade4/ade4-html/dudi.pca.html" rel="nofollow noreferrer">{ade4}</a>.</p>
  
  <p>For pca calculation I selected 40 components while specifying parameters for <code>dudi.pca</code>:</p>
  
  <pre><code>pca = dudi.pca(counts(sce_normalized), scannf=FALSE, nf=40)
  </code></pre>
  
  <p>{Rtsne} gives me an error: “perplexity is too large”, how could it be fixed?</p>
  
  <p>The code I am trying to run is below:</p>
  
  <pre><code>name_of_file &lt;- "dudi_pca.rds"
  path_to_file &lt;- paste0("/scratch/nv4e/scRNA-
  seq/normalization/new_datasets/",
                     name_of_file, sep="")
  dudi_pca &lt;- readRDS(path_to_file)
  
  # run Rtsne with default parameters
  rtsne_out &lt;- Rtsne(as.matrix(dudi_pca), pca=FALSE)
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-21T22:45:28.800Z
Comments.Text: What are the dimensions of `dudi_pca`?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-22T18:30:05.750Z
Comments.Text: The dimensions are `20 000 x 40`
Comments.UserDisplayName: Nikita Vlasenko
Tags: <r><pca>
Title: Perplexity is too large
ThreadText: # Perplexity is too large
  
  (Asked by: username_0 on 2018-01-21)
  
  I am trying to run [{Rtsne}](https://cran.r-project.org/web/packages/Rtsne/Rtsne.pdf). On `pca` dataset prepared by using `dudi.pca` from [{ade4}](https://pbil.univ-lyon1.fr/ade4/ade4-html/dudi.pca.html).
  
  For pca calculation I selected 40 components while specifying parameters for `dudi.pca`:
  
  ```
  pca = dudi.pca(counts(sce_normalized), scannf=FALSE, nf=40)
  
  ```
  
  {Rtsne} gives me an error: “perplexity is too large”, how could it be fixed?
  
  The code I am trying to run is below:
  
  ```
  name_of_file <- "dudi_pca.rds"
  path_to_file <- paste0("/scratch/nv4e/scRNA-
  seq/normalization/new_datasets/",
                     name_of_file, sep="")
  dudi_pca <- readRDS(path_to_file)
  
  # run Rtsne with default parameters
  rtsne_out <- Rtsne(as.matrix(dudi_pca), pca=FALSE)
  
  ```
  
  **Tags:** r, pca
  
  > **Comments:**
  > **username_1**: What are the dimensions of `dudi_pca`?  
  > **username_0**: The dimensions are `20 000 x 40`  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-01-22. Score: 2 | Accepted answer
  
  I was using `dudi_pca` incorrectly. The supplied parameter to `as.matrix()` should have been `dudi_pca$li`:
  
  ```
  rtsne_out <- Rtsne(as.matrix(dudi_pca$li), pca=FALSE)
  
  ```
  
  
  ---
  
  