Extracting expression data from GSE dataset downloaded from GEO

Question

I have downloaded GSE16146 dataset from GEO using GEOquery R package.

I would like to extract "Data table" from downloaded GSE16146.

>library("GEOquery")
>GSE16146 <- getGEO("GSE16146")
>Table(GSE16146)[1:5,]

This returns the following error:

> Table(GSE16146)[1:5,]
Error in (function (classes, fdef, mtable)  :
unable to find an inherited method for function ‘Table’ for signature ‘"list"’

Can anyone help?

Answer 1

According to the manual, all you need to do is:

library('GEOquery')
gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE)

As explanation, getGEO() outputs by default to GSEMatrix=TRUE and returns a list of ExpressionSet objects. You should get what you were looking for with:

Table(GSMList(gseGSE16146)[[1]])[1:5,]

The manual has also a paragraph about this:

The GSE has a metadata section, just like the other classes. However, it doesn’t have a GEODataTable. Instead, it contains two lists, accessible using GPLList and GSMList, that are each lists of GPL and GSM objects.

I tested the code I posted on R 3.3.2 and I get access to the Data Table just fine.

update:

Answering how to extract the actual expression data (not what asked in the original question):

library(GEOquery) 
data = getGEO("GSE16146") 
datExpr = exprs (data[[1]])