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Question: Can BioC still convert exprSet to ExpressionSet?
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gravatar for David Rossell
8.5 years ago by
David Rossell100
David Rossell100 wrote:
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__" > 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]]
ADD COMMENTlink modified 8.5 years ago by Martin Morgan ♦♦ 20k • written 8.5 years ago by David Rossell100
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gravatar for Martin Morgan
8.5 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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
ADD COMMENTlink written 8.5 years ago by Martin Morgan ♦♦ 20k
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/bioinforma tics/bioinformatics-biostatistics-unit [[alternative HTML version deleted]]
ADD REPLYlink written 8.5 years ago by David Rossell100
0
gravatar for Martin Morgan
8.5 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:
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]] > > > _______________________________________________ > Bioconductor > mailing list > [[Bioconductor at 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 -- 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
ADD COMMENTlink written 8.5 years ago by Martin Morgan ♦♦ 20k
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