text: user2005: I am trying to run {Rtsne}. On pca dataset prepared by using dudi.pca from {ade4}.
  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)
  
  
  user2005: 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)
  
  
original_text: 2005: <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>
   2005: <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>
  