<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>

<scrnaseq><gene-expression><sratoolkit><geoquery><geo>
Why am I getting empty expression data from GEO?
# Why am I getting empty expression data from GEO?

(Asked by: username_0 on 2021-04-13)

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...

**Tags:** scrnaseq, gene-expression, sratoolkit, geoquery, geo

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## 0 answers

