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I want to extract the expression matrix from the GSE object in GEOquery.

library(GEOquery)


gse1 <- getGEO("GSE97168",GSEMatrix=TRUE)
datExpr = exprs (gse1[[1]])
datExpr

GSM2553017 GSM2553018 GSM2553019 GSM2553020 GSM2553021 GSM2553022 GSM2553023 GSM2553024 GSM2553025
     GSM2553026


Table(GSMList(gse1)[[1]])[1:5,]

Table(GSMList(gse1)[[1]])[1:5,]
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘GSMList’ for signature ‘"list"’

Table(GPLList(gse1)[[1]])[1:5,]
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘GPLList’ for signature ‘"list"’

Meta(gse1)$description
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘Meta’ for signature ‘"list"’

Columns(gse1)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘Columns’ for signature ‘"list"’

Why it's not working with R version 3.5.1?

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  • $\begingroup$ Welcome to the site. Are you sure this should be working? In the vignette Table is only used to "Look at data associated with the GSM" not to retrieve the data expression data or information about a specific GSM $\endgroup$
    – llrs
    Feb 20, 2019 at 16:18

1 Answer 1

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Use GSEMatrix=FALSE, the information you want appears to be in the soft file, rather than the matrix. Yes, this is moderately annoying since it means you need two objects to describe this particular dataset.

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