Entering edit mode
Mark W Kimpel
▴
830
@mark-w-kimpel-2027
Last seen 10.0 years ago
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_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=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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