qc in simpleaffy
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@mayte-suarez-farinas-2068
Last seen 6.5 years ago
United States
Hi everybody: I am working with R 2.8 and I the function "qc" from simpleaffy is not working: > q<-qc(abatch) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotation", for signature "AffyBatch" I get the same error if: >annotation(abatch) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotation", for signature "AffyBatch" but not if: > abatch at annotation [1] "hgu133a2.db" sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0 Harshlight_1.12.0 altcdfenvs_2.4.0 [5] hypergraph_1.14.0 Biostrings_2.10.16 IRanges_1.0.12 makecdfenv_1.20.0 [9] affyio_1.10.1 beadarray_1.10.0 sma_0.5.15 hwriter_1.0 [13] affycoretools_1.14.1 annaffy_1.14.0 KEGG.db_2.2.5 biomaRt_1.16.0 [17] GOstats_2.8.0 Category_2.8.4 RBGL_1.18.0 GO.db_2.2.5 [21] RSQLite_0.7-1 DBI_0.2-4 graph_1.20.0 limma_2.16.4 [25] affyQCReport_1.20.0 geneplotter_1.20.0 annotate_1.20.1 AnnotationDbi_1.5.18 [29] lattice_0.17-17 RColorBrewer_1.0-2 affyPLM_1.18.1 preprocessCore_1.4.0 [33] xtable_1.5-4 simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 [37] genefilter_1.22.0 survival_2.34-1 affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 RCurl_0.94-1 XML_2.1-0 [6] cluster_1.11.11 grid_2.8.1
GO simpleaffy GO simpleaffy • 768 views
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@martin-morgan-1513
Last seen 3 months ago
United States
Hi Mayte -- Mayte Suarez-Farinas <farinam at="" mail.rockefeller.edu=""> writes: > Hi everybody: > > I am working with R 2.8 and I the function "qc" from simpleaffy is > not working: > > > q<-qc(abatch) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotation", for > signature "AffyBatch" I think IRanges::annotation is masking Biobase::annotation. This might be solved by updating packages, specifically IRanges. Have you tried updating your packages http://bioconductor.org/docs/install/ ? From the prompt I think Biobase::annotation(abatch) will work, and that annotation <- Biobase::annotation qc(abatch) will too. And that R 2.9 / Bioc 2.4will also avoid this problem. Martin > I get the same error if: > > >annotation(abatch) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotation", for > signature "AffyBatch" > > but not if: > > > abatch at annotation > [1] "hgu133a2.db" > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0 Harshlight_1.12.0 > altcdfenvs_2.4.0 > [5] hypergraph_1.14.0 Biostrings_2.10.16 IRanges_1.0.12 > makecdfenv_1.20.0 > [9] affyio_1.10.1 beadarray_1.10.0 sma_0.5.15 > hwriter_1.0 > [13] affycoretools_1.14.1 annaffy_1.14.0 KEGG.db_2.2.5 > biomaRt_1.16.0 > [17] GOstats_2.8.0 Category_2.8.4 RBGL_1.18.0 > GO.db_2.2.5 > [21] RSQLite_0.7-1 DBI_0.2-4 graph_1.20.0 > limma_2.16.4 > [25] affyQCReport_1.20.0 geneplotter_1.20.0 annotate_1.20.1 > AnnotationDbi_1.5.18 > [29] lattice_0.17-17 RColorBrewer_1.0-2 affyPLM_1.18.1 > preprocessCore_1.4.0 > [33] xtable_1.5-4 simpleaffy_2.18.0 gcrma_2.14.1 > matchprobes_1.14.1 > [37] genefilter_1.22.0 survival_2.34-1 affy_1.20.2 > Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 > RCurl_0.94-1 XML_2.1-0 > [6] cluster_1.11.11 grid_2.8.1 > > _______________________________________________ > 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
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@mayte-suarez-farinas-2068
Last seen 6.5 years ago
United States
Hi all! I try what it was suggested from my previous post. But now I get another error: I load only the minimum libraries: here is what i got: library(simpleaffy) load("Batch1-AffyBatch.rda") qcs<-qc(abatch) plot(qcs) Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' so, whats teh problem now?? sessionInfo() R version 2.8.1 (2008-12-22) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.5.18 hgu133plus2cdf_2.3.0 [6] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 genefilter_1.22.0 survival_2.34-1 [11] affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0 On Apr 23, 2009, at 6:59 PM, Chao-Jen Wong wrote: > Hi, Mayte, > > Can you try typing Biobase::annotation(abatch) and see if it still > gives > any error. If not, then that means the "annotation" method may be > crushed by other packages in your search path. It seems to me that you > upload a lot of packages into the workspace. Can you try to leave > the R > environment and call up R again. Don't load too many libraries this > time, only affy and simpleaffy and your affyBatch data object. Hope > that would work. > > Chao-Jen > > Mayte Suarez-Farinas wrote: >> Hi everybody: >> >> I am working with R 2.8 and I the function "qc" from simpleaffy is >> not >> working: >> >>> q<-qc(abatch) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "annotation", for >> signature "AffyBatch" >> >> I get the same error if: >> >>> annotation(abatch) >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "annotation", for >> signature "AffyBatch" >> >> but not if: >> >>> abatch at annotation >> [1] "hgu133a2.db" >> >> >> sessionInfo() >> R version 2.8.1 (2008-12-22) >> i386-apple-darwin8.11.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets methods base >> >> other attached packages: >> [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0 >> Harshlight_1.12.0 altcdfenvs_2.4.0 >> [5] hypergraph_1.14.0 Biostrings_2.10.16 >> IRanges_1.0.12 makecdfenv_1.20.0 >> [9] affyio_1.10.1 beadarray_1.10.0 >> sma_0.5.15 hwriter_1.0 >> [13] affycoretools_1.14.1 annaffy_1.14.0 >> KEGG.db_2.2.5 biomaRt_1.16.0 >> [17] GOstats_2.8.0 Category_2.8.4 >> RBGL_1.18.0 GO.db_2.2.5 >> [21] RSQLite_0.7-1 DBI_0.2-4 >> graph_1.20.0 limma_2.16.4 >> [25] affyQCReport_1.20.0 geneplotter_1.20.0 >> annotate_1.20.1 AnnotationDbi_1.5.18 >> [29] lattice_0.17-17 RColorBrewer_1.0-2 >> affyPLM_1.18.1 preprocessCore_1.4.0 >> [33] xtable_1.5-4 simpleaffy_2.18.0 >> gcrma_2.14.1 matchprobes_1.14.1 >> [37] genefilter_1.22.0 survival_2.34-1 >> affy_1.20.2 Biobase_2.2.2 >> >> loaded via a namespace (and not attached): >> [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 >> RCurl_0.94-1 XML_2.1-0 >> [6] cluster_1.11.11 grid_2.8.1 >> >> _______________________________________________ >> 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 > > > -- > Chao-Jen Wong > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., M2-B876 > PO Box 19024 > Seattle, WA 98109 > 206.667.4485 > cwon2 at fhcrc.org >
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Hi Mayte, Is there some reason not to use arrayQualityMetrics? It gives a much more comprehensive overview of the quality issues that may be present. simpleaffy's QC is reasonable, but is very centered on Affymetric suggested methods. In any event, you are use R 2.8.x and the current releases are 2.9.x, so it might be good to try to upgrade? And finally, if it persists, you will have to find a way for someone else to have access to your data for testing (or show that this happens on one of the more readily available data sets). At the very least, perhaps checking the class of qcs to see what was returned by your call to qc, would be a good start. thanks Robert Mayte Suarez-Farinas wrote: > Hi all! > > > I try what it was suggested from my previous post. But now I get another > error: > I load only the minimum libraries: here is what i got: > > library(simpleaffy) > load("Batch1-AffyBatch.rda") > qcs<-qc(abatch) > plot(qcs) > Error in as.double(y) : > cannot coerce type 'S4' to vector of type 'double' > > so, whats teh problem now?? > > > > sessionInfo() > R version 2.8.1 (2008-12-22) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] hgu133a2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 > AnnotationDbi_1.5.18 hgu133plus2cdf_2.3.0 > [6] simpleaffy_2.18.0 gcrma_2.14.1 matchprobes_1.14.1 > genefilter_1.22.0 survival_2.34-1 > [11] affy_1.20.2 Biobase_2.2.2 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0 > > > > > On Apr 23, 2009, at 6:59 PM, Chao-Jen Wong wrote: > >> Hi, Mayte, >> >> Can you try typing Biobase::annotation(abatch) and see if it still gives >> any error. If not, then that means the "annotation" method may be >> crushed by other packages in your search path. It seems to me that you >> upload a lot of packages into the workspace. Can you try to leave the R >> environment and call up R again. Don't load too many libraries this >> time, only affy and simpleaffy and your affyBatch data object. Hope >> that would work. >> >> Chao-Jen >> >> Mayte Suarez-Farinas wrote: >>> Hi everybody: >>> >>> I am working with R 2.8 and I the function "qc" from simpleaffy is not >>> working: >>> >>>> q<-qc(abatch) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function "annotation", for >>> signature "AffyBatch" >>> >>> I get the same error if: >>> >>>> annotation(abatch) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function "annotation", for >>> signature "AffyBatch" >>> >>> but not if: >>> >>>> abatch at annotation >>> [1] "hgu133a2.db" >>> >>> >>> sessionInfo() >>> R version 2.8.1 (2008-12-22) >>> i386-apple-darwin8.11.1 >>> >>> locale: >>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets methods base >>> >>> other attached packages: >>> [1] hgu133plus2probe_2.3.0 hgu133plus2cdf_2.3.0 >>> Harshlight_1.12.0 altcdfenvs_2.4.0 >>> [5] hypergraph_1.14.0 Biostrings_2.10.16 >>> IRanges_1.0.12 makecdfenv_1.20.0 >>> [9] affyio_1.10.1 beadarray_1.10.0 >>> sma_0.5.15 hwriter_1.0 >>> [13] affycoretools_1.14.1 annaffy_1.14.0 >>> KEGG.db_2.2.5 biomaRt_1.16.0 >>> [17] GOstats_2.8.0 Category_2.8.4 >>> RBGL_1.18.0 GO.db_2.2.5 >>> [21] RSQLite_0.7-1 DBI_0.2-4 >>> graph_1.20.0 limma_2.16.4 >>> [25] affyQCReport_1.20.0 geneplotter_1.20.0 >>> annotate_1.20.1 AnnotationDbi_1.5.18 >>> [29] lattice_0.17-17 RColorBrewer_1.0-2 >>> affyPLM_1.18.1 preprocessCore_1.4.0 >>> [33] xtable_1.5-4 simpleaffy_2.18.0 >>> gcrma_2.14.1 matchprobes_1.14.1 >>> [37] genefilter_1.22.0 survival_2.34-1 >>> affy_1.20.2 Biobase_2.2.2 >>> >>> loaded via a namespace (and not attached): >>> [1] GSEABase_1.4.0 KernSmooth_2.22-22 Matrix_0.999375-21 >>> RCurl_0.94-1 XML_2.1-0 >>> [6] cluster_1.11.11 grid_2.8.1 >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> Chao-Jen Wong >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Avenue N., M2-B876 >> PO Box 19024 >> Seattle, WA 98109 >> 206.667.4485 >> cwon2 at fhcrc.org >> > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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