GEO data sample information error

Question

[Jakpa]

Hi,

I ran the following command in R to download GEO data:

library("GEOquery")
library(affy)
library(oligo)
library("org.Hs.eg.db")

asserId = "GSE32894"
gse = getGEO(asserId)

pData(gse) ## sample data
fData(gse) # gene annotation
exprs(gse)[1,] # expression data

I got this errors:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"character"’

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘fData’ for signature ‘"character"’

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘pData’ for signature ‘"character"’

I have seen some post but not related to GEO. I honestly could not fully understand the errors.

any suggestion on this will be helpful.

Answer 1

[ATpoint]

The getGEO function returns a list, so to access the actual content use gse[[1]], then the commands should work.