[BioC] GeneSetCollection with mogene10sttranscriptcluster solution

[Mary Putt]

Martin

Thanks very much for the suggestion--I needed more detail on the 
annotation package--not just mogene10st.

 > annotation(myAB_rma)<-"mogene10sttranscriptcluster"
 > gsc<-GeneSetCollection(myAB_rma, setType=GOCollection())


Mary

Martin Morgan wrote:
> On 01/27/2011 08:18 AM, Mary Putt wrote:
>   
>> Hi
>>
>> I am trying to create gene sets and have the following mysterious error.
>> Many thanks in advance for suggestions,
>>     
>
> Hi Mary --
>
>   
>> Mary Putt
>>
>>     
>>> search()
>>>       
>> [1] ".GlobalEnv"                           [2]
>> "package:GO.db"                        [3]
>> "package:mogene10sttranscriptcluster.db"
>> [4] "package:org.Mm.eg.db"                 [5]
>> "package:RSQLite"                      [6]
>> "package:DBI"                          [7]
>> "package:affy"                         [8]
>> "package:genefilter"                   [9]
>> "package:GSEABase"                     [10]
>> "package:graph"                        [11]
>> "package:annotate"                     [12]
>> "package:AnnotationDbi"                [13]
>> "package:Biobase"                      [14]
>> "package:stats"                        [15]
>> "package:graphics"                     [16]
>> "package:grDevices"                    [17]
>> "package:utils"                        [18]
>> "package:datasets"                     [19]
>> "package:methods"                      [20]
>> "Autoloads"                            [21]
>> "package:base"                         >
>>     
>>> date()
>>>       
>> [1] "Thu Jan 27 11:23:25 2011"
>>     
>>> setwd("/project/cvi/parmacek/nina_bowens/Rdata")
>>>
>>> load("myAB_rma.Rdata")
>>> class(myAB_rma)
>>>       
>> [1] "ExpressionSet"
>> attr(,"package")
>> [1] "Biobase"
>>     
>>> objects()
>>>       
>> [1] "e_set"    "myAB_rma"
>>     
>>> gsc<-GeneSetCollection(myAB_rma, setType=GOCollection())
>>>       
>> Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) :
>>  error in evaluating the argument 'x' in selecting a method for function
>> 'as.list'
>>     
>>> traceback()
>>>       
>> 3: as.list(getAnnMap("GO2PROBE", annotation(idType)))
>> 2: GeneSetCollection(myAB_rma, setType = GOCollection())
>> 1: GeneSetCollection(myAB_rma, setType = GOCollection())
>>     
>
> I think the problem is that myAB_rma does not contain enough information
> to create the gene set, for instance as when the 'annotation' slot of
> sample.ExpressionSet is assigned a non-existent chip:
>
>   
>> data(sample.ExpressionSet)
>> annotation(sample.ExpressionSet)
>>     
> [1] "hgu95av2"
>   
>> gsc <- GeneSetCollection(sample.ExpressionSet, setType=GOCollection())
>> annotation(sample.ExpressionSet)="foo"
>> GeneSetCollection(sample.ExpressionSet, setType=GOCollection())
>>     
> Error in as.list(getAnnMap("GO2PROBE", annotation(idType))) :
>   error in evaluating the argument 'x' in selecting a method for
> function 'as.list'
>
> Martin
>
>   
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>>     
>
>
>