[BioC] cannot access annotation from ExpressionSet in Bioc-Devel

[Kasper Daniel Hansen]

This was discussed at length on Bioc-Devel recently. The reason is  
that IRanges also defines annotation and that it in this case masks  
the annotation method from Biobase.

No solution seems to be forthcoming, based on that rather unfortunate  
discussion. Prepare yourself for a life of typing Biobase:annotation  
instead.

Kasper

On Feb 23, 2009, at 17:52 , Mark Kimpel wrote:

> I have a function that has run well for several years and suddenly  
> tonight
> it blew up, unable to access the annotation slot of an  
> ExpressionSet. Does
> annotation(myExpressionSet) no longer work?
>
> Below is my output with my sessionInfo(). You will see that I am  
> have an
> ExpressionSet with $annotation equal to "rat2302". What's up? Mark
>
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "annotation", for
> signature "ExpressionSet"
>
> Enter a frame number, or 0 to exit
>
> 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1,
> custom.contra
> 2: annotation(AOP$eSet)
> 3: function (classes, fdef, mtable)
>
> Selection: 1
> Called from: eval(expr, envir, enclos)
> Browse[1]> attributes(AOP$eSet)
> $.__classVersion__
>            R       Biobase          eSet ExpressionSet
>      "2.9.0"      "2.3.10"       "1.1.0"       "1.0.0"
>
> $assayData
> <environment: 0x2ed74c80>
>
> $phenoData
> An object of class "AnnotatedDataFrame"
>  sampleNames: BB02R001.CEL, BB02R002.CEL, ..., BB02R048.CEL  (48  
> total)
>  varLabels and varMetadata description:
>    SampleNames:
>    Tube:
>    ...: ...
>    Lab.Hyb: NA
>    (11 total)
>
> $featureData
> An object of class "AnnotatedDataFrame"
>  featureNames: 1367452_at, 1367453_at, ..., AFFX-TrpnX-M_at  (31099  
> total)
>  varLabels and varMetadata description: none
>
> $experimentData
> Experiment data
>  Experimenter name:
>  Laboratory:
>  Contact information:
>  Title:
>  URL:
>  PMIDs:
>  No abstract available.
>  Information is available on: preprocessing
>  notes:
>   :
>
>
> $annotation
> [1] "rat2302"
>
> $class
> [1] "ExpressionSet"
> attr(,"package")
> [1] "Biobase"
>
> Browse[1]> AOP$eSet$annotation
> NULL
> Browse
>
> Enter a frame number, or 0 to exit
>
> 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1,
> custom.contra
> 2: annotation(AOP$eSet)
> 3: function (classes, fdef, mtable)
>
> Selection: 1
> Called from: eval(expr, envir, enclos)
> Browse[1]> annotation(AOP$eSet)
> Error during wrapup: unable to find an inherited method for function
> "annotation", for signature "ExpressionSet"
> Browse[1]> experimentData(AOP$eSet)
> Experiment data
>  Experimenter name:
>  Laboratory:
>  Contact information:
>  Title:
>  URL:
>  PMIDs:
>  No abstract available.
>  Information is available on: preprocessing
>  notes:
>   :
>
> Browse[1]> sessionInfo()
> R version 2.9.0 Under development (unstable) (2009-01-04 r47472)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_NUMERIC 
> = 
> C 
> ;LC_TIME 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_COLLATE 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_MONETARY 
> = 
> C 
> ;LC_MESSAGES 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_PAPER 
> = 
> en_US 
> .UTF 
> -8 
> ;LC_NAME 
> = 
> C 
> ;LC_ADDRESS 
> =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets   
> methods
> [8] base
>
> other attached packages:
> [1] qvalue_1.17.0        limma_2.17.10        affyQCReport_1.21.1
> [4] geneplotter_1.21.2   lattice_0.17-20      annotate_1.21.4
> [7] RColorBrewer_1.0-2   affyPLM_1.19.7       preprocessCore_1.5.3
> [10] xtable_1.5-4         simpleaffy_2.19.3    gcrma_2.15.3
> [13] matchprobes_1.15.5   Biostrings_2.11.32   IRanges_1.1.40
> [16] genefilter_1.23.2    rat2302cdf_2.3.0     affycoretools_1.15.4
> [19] KEGG.db_2.2.5        GO.db_2.2.5          RSQLite_0.7-1
> [22] DBI_0.2-4            AnnotationDbi_1.5.16 affy_1.21.7
> [25] Biobase_2.3.10       graph_1.21.4
>
> loaded via a namespace (and not attached):
> [1] affyio_1.11.3      annaffy_1.15.0     biomaRt_1.99.5
> Category_2.9.11
> [5] cluster_1.11.12    GOstats_2.9.2      grid_2.9.0
> GSEABase_1.5.2
> [9] KernSmooth_2.22-22 RBGL_1.19.2        RCurl_0.94-1
> splines_2.9.0
> [13] survival_2.34-1    tools_2.9.0        XML_2.1-0
> Browse[1]>
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do."  
> -- B.
> F. Skinner
> ******************************************************************
>
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