Thank you Martin, I tried it but it still doesn't work (see below).

Anyway, I managed to get access to the raw data so I guess it'll just be
easier to build the ExpressionSet from scratch. Thanks for your help!

David

> str(oncogene)
 list()
 - attr(*, "exprs")= num [1:22283, 1:24] 9.53 6.73 5.53 7.99 3.38 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:22283] "1007_s_at" "1053_at" "117_at" "121_at" ...
  .. ..$ : chr [1:24] "P1" "P2" "P3" "P4" ...
 - attr(*, "se.exprs")= logi[0 , 0 ]
 - attr(*, "description")= list()
  ..- attr(*, "name")= chr ""
  ..- attr(*, "lab")= chr ""
  ..- attr(*, "contact")= chr ""
  ..- attr(*, "title")= chr ""
  ..- attr(*, "abstract")= chr ""
  ..- attr(*, "url")= chr ""
  ..- attr(*, "pubMedIds")= chr ""
  ..- attr(*, "samples")= list()
  ..- attr(*, "hybridizations")= list()
  ..- attr(*, "normControls")= list()
  ..- attr(*, "preprocessing")= list()
  ..- attr(*, "other")= list()
  ..- attr(*, "class")= atomic [1:1] MIAME
  .. ..- attr(*, "package")= chr "Biobase"
 - attr(*, "annotation")= chr ""
 - attr(*, "notes")= chr ""
 - attr(*, "reporterInfo")= symbol NULL
 - attr(*, "phenoData")= list()
  ..- attr(*, "pData")='data.frame':    24 obs. of  1 variable:
  .. ..$ recurrence: Factor w/ 2 levels "N","Y": 1 1 1 1 1 1 1 1 1 1 ...
  ..- attr(*, "varLabels")=List of 1
  .. ..$ recurence: chr "Recurence within 5 years"
  ..- attr(*, "varMetadata")='data.frame':    0 obs. of  0 variables
  ..- attr(*, "class")= atomic [1:1] phenoData
  .. ..- attr(*, "package")= chr "Biobase"
 - attr(*, "class")= atomic [1:1] exprSet
  ..- attr(*, "package")= chr "Biobase"

> attr(oncogene, "description") = list()
> as(oncogene, "ExpressionSet")
Error in asMethod(object) :
  trying to get slot "description" from an object (class "exprSet") that is
not an S4 object



On Tue, May 12, 2009 at 5:40 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi David --
>
> David Rossell <david.rossell@irbbarcelona.org> writes:
>
> > Dear all, I'm getting an error message when trying to convert an old
> exprSet
> > object to the ExpressionSet class. "oncogene" is an exprSet object that I
> > first load.
> >
> >> class(oncogene)
> > [1] "exprSet"
> > attr(,"package")
> > [1] "Biobase"
> >
> >> slotNames(oncogene)
> > [1] "exprs"             "se.exprs"          "description"
> > [4] "annotation"        "notes"             "reporterInfo"
> > [7] "phenoData"         ".__classVersion__"
>
> slotNames consults the class definition, so is not really helfpul. I
> think str(oncogene) will show the old-style list + attributes.
>
> There's an archived instance in
>
> fl <- system.file("UnitTests", "VersionedClass_data", "1.8",
>                  "exprSet.Rda", package="Biobase")
>
> but I think your version predates 1.8. Can you
>
>  attr(oncogene, "description") = list()
>  as(oncogene, "ExpressionSet")
>
> ? Likely some warnings...
>
> Martin
>
> >> newoncogene <- as(oncogene,"ExpressionSet")
> > Error in asMethod(object) :
> >   trying to get slot "description" from an object (class "exprSet") that
> is
> > not an S4 object
> >
> > So the usual "as" conversion doesn't seem to work. Actually I'm not even
> > allowed to manually access any of the slots, so I can't even create the
> > ExpressionSet extracting each piece of information carefully.
> >
> >> oncogene@annotation
> > Error: trying to get slot "annotation" from an object (class "exprSet")
> that
> > is not an S4 object
> >
> >> head(oncogene@exprs)
> > Error: trying to get slot "exprs" from an object (class "exprSet") that
> is
> > not an S4 object
> > Error in head(oncogene@exprs) :
> >   error in evaluating the argument 'x' in selecting a method for function
> > 'head'
> >
> >> head(exprs(oncogene))
> > Error in function (classes, fdef, mtable)  :
> >   unable to find an inherited method for function "exprs", for signature
> > "exprSet"
> > Error in head(exprs(oncogene)) :
> >   error in evaluating the argument 'x' in selecting a method for function
> > 'head'
> >
> > I haven't found this problem posted anywhere. I know that exprSet has
> been
> > deprecated but the conversion method should still work right?
> > My session info is below, thanks in advance for any hints,
> >
> > David
> >
> >> sessionInfo()
> > R version 2.8.1 (2008-12-22)
> > i386-apple-darwin8.11.1
> >
> > locale:
> > C
> >
> > attached base packages:
> > [1] splines   tools     stats     graphics  grDevices utils     datasets
> > [8] methods   base
> >
> > other attached packages:
> >  [1] convert_1.18.0       marray_1.20.0        MDA_1.0.1
> >  [4] Heatplus_1.12.0      mouse4302.db_2.2.5   hgu133a.db_2.2.5
> >  [7] hgu133plus2.db_2.2.5 RSQLite_0.7-1        DBI_0.2-4
> > [10] biomaRt_1.16.0       hopach_2.3.0         gaga_1.1.1
> > [13] coda_0.13-4          lattice_0.17-17      ada_2.0-1
> > [16] sma_0.5.15           randomForest_4.5-28  ClassDiscovery_2.5.0
> > [19] PreProcess_2.5.0     oompaBase_2.5.0      gplots_2.6.0
> > [22] gdata_2.4.2          gtools_2.5.0         limma_2.16.5
> > [25] MLInterfaces_1.22.0  cluster_1.11.11      annotate_1.20.1
> > [28] xtable_1.5-5         AnnotationDbi_1.4.2  rda_1.0
> > [31] rpart_3.1-42         genefilter_1.22.0    survival_2.34-1
> > [34] MASS_7.2-45          Biobase_2.2.2
> >
> > loaded via a namespace (and not attached):
> > [1] RCurl_0.93-0 XML_1.99-0   grid_2.8.1
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
David Rossell, PhD
Manager, Bioinformatics and Biostatistics unit
IRB Barcelona
Tel (+34) 93 402 0217
Fax (+34) 93 402 0257

http://www.irbbarcelona.org/index.php/en/research/platforms/bioinformatics/bioinformatics-biostatistics-unit

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