0 Features for COVID-19 ExpressionSet through GEOQuery

Question

[arjuncsubra]

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?

Answer 1

[Kevin Blighe]

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:

• https://ftp.ncbi.nlm.nih.gov/geo/series/GSE150nnn/GSE150728/suppl/

Kevin

[H. Z. Amini]

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.

[Kevin Blighe]

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

[H. Z. Amini]

Thank you for your reply.

Answer 2

[Alana]

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

[Sean Davis]

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