> Dear All,
>
> I am trying to analyze a Microarray series data using "GEOquery". I
> get the below
> error when trying to extract the information.
>
> > gse = getGEO("GSE15709");
> > Meta(gse)
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "Meta", for signature
> "list"
> > GSMList(gse)[[1]]
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "GSMList", for
> signature "list"
>
> Thanks in advance for your help.
>
>
getGEO() defaults to GSEMatrix=TRUE. Per the documentation, this returns a
list of ExpressionSet objects. So, gse[[1]] is an ExpressionSet. The
accessors that you are using above are for returns from calls to getGEO()
with GSEMatrix=FALSE. Unless there is a specific need to get information
from the full GSE SOFT file, I would recommend staying with GSEMatrix=TRUE
and working with the more standard ExpressionSet object(s).
Hope that helps.
Sean
#########################
B = as(gse[[1]],"ExpressionSet")
then good to go.
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