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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