text: user6339: I am trying to analyze the scRNAseq data from this study. In their Method section they write:
  
  The accession number for the RNA and DNaseq data reported in this
  paper is GEO:
  GSE116237.
  
  When I go ahead and try to pull this data in R using GEOquery, I am faced with a data frame with no features (i.e. no genes). The following code
  library("GEOquery")
  gse <- getGEO("GSE116237")
  eset1 <- gse[[1]]
  eset2 <- gse[[2]]
  
  print(dim(eset1))
  print(dim(eset2))
  
  yields
  Features  Samples 
         0      184 
  Features  Samples 
         0      681 
  
  I also didn't manage to download the data manually; I get an error message when trying to unzip the .zip files or get redirected to SRA Run Selector from which I also didn't manage to figure out how to download stuff.
  Am I missing something or are these files simply corrupted? The paper is published in Cell, so I would assume this data is, to some extend, legit...
  
  user-1: I am sure the data is legit, you are just approaching it incorrectly. getGEO is an application for microarray data, not for digital count data such as (sc)RNA-seq, therefore what you aim to do is simply not possible by design. Unless you want to start from the raw reads why not taking the at the file named GSE116237_scRNAseq_expressionMatrix.txt.gz provided at the bottom of https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116237?
  
original_text: 6339: <p>I am trying to analyze the scRNAseq data from <a href="https://www.sciencedirect.com/science/article/pii/S0092867418307931?via%3Dihub" rel="nofollow noreferrer">this study</a>. In their Method section they write:</p>
  <blockquote>
  <p>The accession number for the RNA and DNaseq data reported in this
  paper is GEO:
  <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116237" rel="nofollow noreferrer">GSE116237</a>.</p>
  </blockquote>
  <p>When I go ahead and try to pull this data in R using <code>GEOquery</code>, I am faced with a data frame with no features (i.e. no genes). The following code</p>
  <pre><code>library(&quot;GEOquery&quot;)
  gse &lt;- getGEO(&quot;GSE116237&quot;)
  eset1 &lt;- gse[[1]]
  eset2 &lt;- gse[[2]]
  
  print(dim(eset1))
  print(dim(eset2))
  </code></pre>
  <p>yields</p>
  <pre><code>Features  Samples 
         0      184 
  Features  Samples 
         0      681 
  </code></pre>
  <p>I also didn't manage to download the data manually; I get an error message when trying to unzip the <code>.zip</code> files or <a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA477841&amp;o=acc_s%3Aa" rel="nofollow noreferrer">get redirected to SRA Run Selector</a> from which I also didn't manage to figure out how to download stuff.</p>
  <p>Am I missing something or are these files simply corrupted? The paper is published in Cell, so I would assume this data is, to some extend, legit...</p>
   -1: <p>I am sure the data is legit, you are just approaching it incorrectly. getGEO is an application for microarray data, not for digital count data such as (sc)RNA-seq, therefore what you aim to do is simply not possible by design. Unless you want to start from the raw reads why not taking the at the file named <code>GSE116237_scRNAseq_expressionMatrix.txt.gz</code> provided at the bottom of <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116237" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116237</a>?</p>
  