> 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
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B = as(gse[[1]],"ExpressionSet")
then good to go.
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