Question: 0 Features for COVID-19 ExpressionSet through GEOQuery
0
gravatar for arjuncsubra
3 months ago by
arjuncsubra0 wrote:

Hi all,

Disclaimer: I am very new to Bioconductor.

I am analyzing the GEO dataset "GSE150728" or " A single-cell atlas of the peripheral immune response to severe COVID-19".

In doing this, I ran the getGEO command on this accession number.

library(GEOquery)
covid_data <- getGEO("GSE150728")
covid_data #for viewing

I viewed covid_data and found out it was an ExpressionSet, but seemed to have zero features, yet 13 samples. Here is the result I got:

File stored at: 
C:\Users\arjun\AppData\Local\Temp\RtmpETJztZ/GPL24676.soft
$GSE150728_series_matrix.txt.gz
ExpressionSet (storageMode: lockedEnvironment)
assayData: 0 features, 13 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: GSM4557327 GSM4557328 ... GSM4557339
    (13 total)
  varLabels: title geo_accession ... sample origin:ch1
    (41 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 32514174 
Annotation: GPL24676

My main goal for this dataset is to create clustering maps.

What do I need to do to make this expression set non-empty? If I have to manually load different pieces of data, what is the process?

rna-seq geoquery R • 171 views
ADD COMMENTlink modified 3 months ago by Kevin Blighe66k • written 3 months ago by arjuncsubra0
1
gravatar for Kevin Blighe
3 months ago by
Kevin Blighe66k
Kevin Blighe66k wrote:

The Series Matrix File for the dataset is empty, so, you won't be able to use GEOquery. For RNA-seq studies, typically, GEOquery cannot be used.

You can download the available Rds files that are available via the tar file:

Kevin

ADD COMMENTlink written 3 months ago by Kevin Blighe66k
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