[BioC] Can BioC still convert exprSet to ExpressionSet?

Martin Morgan mtmorgan at fhcrc.org
Wed May 13 05:19:55 CEST 2009


David Rossell <david.rossell at irbbarcelona.org> writes:

> 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

OK after some investigation I see that coerce,exprSet-method was
updated during the last release cycle, and in the current R (2.9) /
Biobase (2.4) a simple

  as(oncogene, "ExpressionSet")

should work.

Martin

>
>
> On Tue, May 12, 2009 at 5:40 PM, Martin Morgan <[[mtmorgan at fhcrc.org]]> wrote:
>
>           Hi David --     
>
>                David Rossell <[[david.rossell at 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 at annotation     > Error:
>      trying to get slot "annotation" from an object (class "exprSet")
>      that     > is not an S4 object     >     >> head(oncogene at exprs)     >
>      Error: trying to get slot "exprs" from an object (class "exprSet")
>      that is     > not an S4 object     > Error in head(oncogene at 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]]     >     >
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>      --     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     

-- 
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



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