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

gse <- getGEO("GSE116237")
eset1 <- gse[[1]]
eset2 <- gse[[2]]



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...


1 Answer 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?


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