GEOquery using keywords in R
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Didi ▴ 10
@didi-10905
Last seen 2.1 years ago
Spain

Hi,

How to do a GEO query using keywords in R?

I found a few publications but they use the GSE accession number:

GEO_DATASETS <- c("GSE73835")

eset <- getGEOdataObjects(GEO_DATASETS[1])

eset

 

Thanks a lot.

D.

GEO geoquery geometadb • 1.4k views
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What exactly are you asking? You say something about keywords, but then you try to use a GSE ID, using a non-existent function.
 

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I don't know if it's possible instead of using GSE accession numbers to use keywords like c("arabidopsis", "drought") and get all the related GSE accesion numbers. Is there any way to do that?
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You could either use the Bioconductor GEOmetadb package, a web interface query on the NCBI website, or eUtils. There are other third-party options as well as similar functionality at EBI.

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@sean-davis-490
Last seen 12 weeks ago
United States

Just guessing that this is what you want:

library(GEOquery)
eset = getGEO('GSE73835')[[1]]
eset
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