how to get all information of a platform for all samples using GEOquery
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Nemo ▴ 80
@nemo-7332
Last seen 3.6 years ago
India

Hello, 

I am trying to collect information of all samples but i don't know how to get all information for all samples.

I tired the following, is there a better way to do that ? 

gpl <- getGEO("GPL16791")
data <- gpl@header$sample_id
getInfo <- function(x){
      gps <- getGEO(x)
      gps <- unlist(gps@header)
      gps <- data.frame(gps, stringsAsFactors = F)
      gps <- t(gps)
      gps <- unique(gps)
      return(gps)
}
dat <- lapply(data, FUN = getInfo)

 

geoquery r • 1.4k views
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@sean-davis-490
Last seen 14 days ago
United States

Check out the GEOmetadb package.  

library(GEOmetadb)
s = getSQLiteFile()
con = dbConnect(SQLite(),s)
res = dbGetQuery(con,"select gsm,title,gpl from gsm where gpl='GPL16791'")
dim(res)
head(res)
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@Sean Davis Thanks for your message! I see you are the author! Can you please give me the example how to get all sample information of above platform for example using GEOmetadb ? I looked at the example provided by the package but it is chinese to me :-p 

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Edited to include code....

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