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
