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?