Question

GEOquery using keywords in R

0

Entering edit mode

Didi ▴ 10

@didi-10905

Last seen 2.7 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 • 1.7k views

ADD COMMENT • link updated 6.5 years ago by Sean Davis 21k • written 6.5 years ago by Didi ▴ 10

0

Entering edit mode

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 REPLY • link 6.5 years ago James W. MacDonald 67k

0

Entering edit mode

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 REPLY • link 6.5 years ago Didi ▴ 10

0

Entering edit mode

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 REPLY • link 6.5 years ago Sean Davis 21k

score 0 · Answer 1 · 2018-06-04

0

Entering edit mode

Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

Just guessing that this is what you want:

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

ADD COMMENT • link 6.5 years ago Sean Davis 21k