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Question: GEOquery using keywords in R
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gravatar for Didi
5 months ago by
Didi10
Didi10 wrote:

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.

ADD COMMENTlink modified 5 months ago by Sean Davis21k • written 5 months ago by Didi10

What exactly are you asking? You say something about keywords, but then you try to use a GSE ID, using a non-existent function.
 

ADD REPLYlink written 5 months ago by James W. MacDonald48k
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?
ADD REPLYlink modified 5 months ago • written 5 months ago by Didi10

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.

ADD REPLYlink written 5 months ago by Sean Davis21k
0
gravatar for Sean Davis
5 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Just guessing that this is what you want:

library(GEOquery)
eset = getGEO('GSE73835')[[1]]
eset
ADD COMMENTlink written 5 months ago by Sean Davis21k
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