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0 Features for COVID-19 ExpressionSet through GEOQuery

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 r geoquery
• 3,647 views • link
updated by Sean Davis Sean Davis • written by arjuncsubra • arjuncsubra

2 answers

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

• 0 views • link
written by Kevin Blighe Kevin Blighe

Dear Kevin, Thank you for the hint. Would you please explain me more how to do the process? Actually I'm very new in this BIOdata field and I dont know exactly what to do. For my data (GSE81540), I dont have "_Raw.tar" part in the GEO website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81540

So I'm wondering what should I do?

Appreciate your help.

• 0 views • link
written by H. Z. Amini • H. Z. Amini

Hi, I can neither find the data for that study. I think that you should send an email to the contact author (e-mail on GEO accession page). It is possible that a counts matrix is available in the Supplementary Material of the published work

• 0 views • link
written by Kevin Blighe Kevin Blighe

Do you know some other package to analyse RNA-seq data?

• 0 views • link
written by Alana • Alana

Hi, @lessinh4. You should ask a new question and include specifics of what you want to do in it.

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written by Sean Davis Sean Davis

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