According to the manual, all you need to do is:
gseGSE16146 <- getGEO('GSE16146', GSEMatrix=FALSE)
getGEO() outputs by default to
GSEMatrix=TRUE and returns a list of
ExpressionSet objects. You should get what you were looking for with:
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.
Answering how to extract the actual expression data (not what asked in the original question):
data = getGEO("GSE16146")
datExpr = exprs (data[])