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Question: error with accessing GEOquery data
1
gravatar for Kishor Tappita
8.2 years ago by
Kishor Tappita340 wrote:
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. Regards, Kishor
ADD COMMENTlink modified 8.2 years ago by Sean Davis21k • written 8.2 years ago by Kishor Tappita340
2
gravatar for Sean Davis
8.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Sep 1, 2009 at 5:48 AM, Kishor Tappita <kishor.tappita@gmail.com>wrote: > 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 [[alternative HTML version deleted]]
ADD COMMENTlink written 8.2 years ago by Sean Davis21k
Dear Sean, This information does help me a lot. Thank you so much. Regards, Kishor On Tue, Sep 1, 2009 at 3:54 PM, Sean Davis<seandavi at="" gmail.com=""> wrote: > > > On Tue, Sep 1, 2009 at 5:48 AM, Kishor Tappita <kishor.tappita at="" gmail.com=""> > wrote: >> >> 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 > >
ADD REPLYlink written 8.2 years ago by Kishor Tappita340
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