[BioC] GeneSetCollection with mogene10sttranscriptcluster

[Martin Morgan]

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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