Answers.Body: <p>You simply need to transform your data.frame into a matrix. Just use these  two lines: </p>
  
  <pre><code>library(SingleCellExperiment)
  sce &lt;- SingleCellExperiment(assays = list(counts = as.matrix(all.counts)))
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-03-04T16:33:02.677Z
Answers.LastActivityDate: 2019-03-04T16:33:02.677Z
Answers.UserDisplayName: M. Aburidi
Answers.Body: <p>I think you might want to use <a href="https://www.bioconductor.org/help/workflows/simpleSingleCell/" rel="nofollow noreferrer">the most recent workflow</a>, which should be for the latest version on Bioconductor.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-12-12T11:21:52.930Z
Answers.LastActivityDate: 2017-12-12T12:53:10.413Z
Answers.LastEditDate: 2017-12-12T12:53:10.413Z
Answers.UserDisplayName: Nils
Body: <p>I am trying to go through the following <a href="https://f1000research.com/articles/5-2122/v2" rel="nofollow noreferrer">scRNA-seq tutorial</a>.</p>
  
  <p>But the line <code>sce &lt;- newSCESet(countData=all.counts)</code> is not working anymore with the most up-to-date version of <code>scater</code>. Now we should use <code>SingleCellExperiment</code> function instead, so when trying to do the following:</p>
  
  <pre><code>sce &lt;- SingleCellExperiment(assays = list(counts = all.counts))
  </code></pre>
  
  <p>I am getting the error: </p>
  
  <pre><code>Error in seq_len(ncol(assay)) : 
    argument must be coercible to non-negative integer
  In addition: Warning message:
  In seq_len(ncol(assay)) : first element used of 'length.out' argument
  </code></pre>
  
  <p>Any help would be greatly appreciated.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-11T08:41:16.030Z
Comments.Text: You can better ask questions about bioconductor packages on [https://support.bioconductor.org/](https://support.bioconductor.org/), you'll probably get an answer from Aaron Lun himself within a day.
Comments.UserDisplayName: benn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-11T09:05:01.960Z
Comments.Text: Which version of R and of the packages are you using? That workflow is for version 3.4 of Bioconductor, and the current  version is 3.6
Comments.UserDisplayName: llrs
Tags: <r><rna-seq>
Title: scater: SingleCellExperiment, Error in seq_len(ncol(assay))
ThreadText: # scater: SingleCellExperiment, Error in seq_len(ncol(assay))
  
  (Asked by: username_0 on 2017-12-10)
  
  I am trying to go through the following [scRNA-seq tutorial](https://f1000research.com/articles/5-2122/v2).
  
  But the line `sce <- newSCESet(countData=all.counts)` is not working anymore with the most up-to-date version of `scater`. Now we should use `SingleCellExperiment` function instead, so when trying to do the following:
  
  ```
  sce <- SingleCellExperiment(assays = list(counts = all.counts))
  
  ```
  
  I am getting the error:
  
  ```
  Error in seq_len(ncol(assay)) : 
    argument must be coercible to non-negative integer
  In addition: Warning message:
  In seq_len(ncol(assay)) : first element used of 'length.out' argument
  
  ```
  
  Any help would be greatly appreciated.
  
  **Tags:** r, rna-seq
  
  > **Comments:**
  > **username_1**: You can better ask questions about bioconductor packages on [https://support.bioconductor.org/](https://support.bioconductor.org/), you'll probably get an answer from Aaron Lun himself within a day.  
  > **username_2**: Which version of R and of the packages are you using? That workflow is for version 3.4 of Bioconductor, and the current  version is 3.6  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2017-12-12. Score: 5 | Accepted answer
  
  I think you might want to use [the most recent workflow](https://www.bioconductor.org/help/workflows/simpleSingleCell/), which should be for the latest version on Bioconductor.
  
  
  ---
  
  ### Answer by username_3 on 2019-03-04. Score: 1
  
  You simply need to transform your data.frame into a matrix. Just use these two lines:
  
  ```
  library(SingleCellExperiment)
  sce <- SingleCellExperiment(assays = list(counts = as.matrix(all.counts)))
  
  ```
  
  
  ---
  
  