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

Tue Feb 24 03:15:59 CET 2009

Hi Mark,
  This has been discussed already - it is worth searching the archives
prior to posting.
You can easily diagnose the problem by using:

> find("annotation")
[1] "package:IRanges" "package:Biobase"

the problem is that both IRanges and Biobase define functions named
IRanges and you must specify which one you want in your script
(Biobase::annotation), or if it is in someone's package then they need
to import the one they want by using a namespace.  In general, one
should not rely on a fortuitous ordering of the search list, nor too
much on unique names for things - there are very few reserved words in
R.

 Also, I don't think it is
> ExpressionSet with $annotation equal to "rat2302". What's up? Mark
these are likely to be S4 objects so the $ part is not correct.

best wishes
   Robert

On Mon, Feb 23, 2009 at 5:52 PM, Mark Kimpel <mwkimpel at gmail.com> 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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org