I have a function that has run well for several years and suddenly tonight it blew up, unable to access the annotation slot of an ExpressionSet. Does annotation(myExpressionSet) no longer work? Below is my output with my sessionInfo(). You will see that I am have an ExpressionSet with $annotation equal to "rat2302". What's up? Mark Error in function (classes, fdef, mtable) : unable to find an inherited method for function "annotation", for signature "ExpressionSet" Enter a frame number, or 0 to exit 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, custom.contra 2: annotation(AOP$eSet) 3: function (classes, fdef, mtable) Selection: 1 Called from: eval(expr, envir, enclos) Browse[1]> attributes(AOP$eSet) $.__classVersion__ R Biobase eSet ExpressionSet "2.9.0" "2.3.10" "1.1.0" "1.0.0" $assayData <environment: 0x2ed74c80=""> $phenoData An object of class "AnnotatedDataFrame" sampleNames: BB02R001.CEL, BB02R002.CEL, ..., BB02R048.CEL (48 total) varLabels and varMetadata description: SampleNames: Tube: ...: ... Lab.Hyb: NA (11 total) $featureData An object of class "AnnotatedDataFrame" featureNames: 1367452_at, 1367453_at, ..., AFFX-TrpnX-M_at (31099 total) varLabels and varMetadata description: none $experimentData Experiment data Experimenter name: Laboratory: Contact information: Title: URL: PMIDs: No abstract available. Information is available on: preprocessing notes: : $annotation [1] "rat2302" $class [1] "ExpressionSet" attr(,"package") [1] "Biobase" Browse[1]> AOP$eSet$annotation NULL Browse Enter a frame number, or 0 to exit 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, custom.contra 2: annotation(AOP$eSet) 3: function (classes, fdef, mtable) Selection: 1 Called from: eval(expr, envir, enclos) Browse[1]> annotation(AOP$eSet) Error during wrapup: unable to find an inherited method for function "annotation", for signature "ExpressionSet" Browse[1]> experimentData(AOP$eSet) Experiment data Experimenter name: Laboratory: Contact information: Title: URL: PMIDs: No abstract available. Information is available on: preprocessing notes: : Browse[1]> sessionInfo() R version 2.9.0 Under development (unstable) (2009-01-04 r47472) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] qvalue_1.17.0 limma_2.17.10 affyQCReport_1.21.1 [4] geneplotter_1.21.2 lattice_0.17-20 annotate_1.21.4 [7] RColorBrewer_1.0-2 affyPLM_1.19.7 preprocessCore_1.5.3 [10] xtable_1.5-4 simpleaffy_2.19.3 gcrma_2.15.3 [13] matchprobes_1.15.5 Biostrings_2.11.32 IRanges_1.1.40 [16] genefilter_1.23.2 rat2302cdf_2.3.0 affycoretools_1.15.4 [19] KEGG.db_2.2.5 GO.db_2.2.5 RSQLite_0.7-1 [22] DBI_0.2-4 AnnotationDbi_1.5.16 affy_1.21.7 [25] Biobase_2.3.10 graph_1.21.4 loaded via a namespace (and not attached): [1] affyio_1.11.3 annaffy_1.15.0 biomaRt_1.99.5 Category_2.9.11 [5] cluster_1.11.12 GOstats_2.9.2 grid_2.9.0 GSEABase_1.5.2 [9] KernSmooth_2.22-22 RBGL_1.19.2 RCurl_0.94-1 splines_2.9.0 [13] survival_2.34-1 tools_2.9.0 XML_2.1-0 Browse[1]> ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]

This was discussed at length on Bioc-Devel recently. The reason is that IRanges also defines annotation and that it in this case masks the annotation method from Biobase. No solution seems to be forthcoming, based on that rather unfortunate discussion. Prepare yourself for a life of typing Biobase:annotation instead. Kasper On Feb 23, 2009, at 17:52 , Mark Kimpel wrote: > I have a function that has run well for several years and suddenly > tonight > it blew up, unable to access the annotation slot of an > ExpressionSet. Does > annotation(myExpressionSet) no longer work? > > Below is my output with my sessionInfo(). You will see that I am > have an > ExpressionSet with $annotation equal to "rat2302". What's up? Mark > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotation", for > signature "ExpressionSet" > > Enter a frame number, or 0 to exit > > 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, > custom.contra > 2: annotation(AOP$eSet) > 3: function (classes, fdef, mtable) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> attributes(AOP$eSet) > $.__classVersion__ > R Biobase eSet ExpressionSet > "2.9.0" "2.3.10" "1.1.0" "1.0.0" > > $assayData > <environment: 0x2ed74c80=""> > > $phenoData > An object of class "AnnotatedDataFrame" > sampleNames: BB02R001.CEL, BB02R002.CEL, ..., BB02R048.CEL (48 > total) > varLabels and varMetadata description: > SampleNames: > Tube: > ...: ... > Lab.Hyb: NA > (11 total) > > $featureData > An object of class "AnnotatedDataFrame" > featureNames: 1367452_at, 1367453_at, ..., AFFX-TrpnX-M_at (31099 > total) > varLabels and varMetadata description: none > > $experimentData > Experiment data > Experimenter name: > Laboratory: > Contact information: > Title: > URL: > PMIDs: > No abstract available. > Information is available on: preprocessing > notes: > : > > > $annotation > [1] "rat2302" > > $class > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" > > Browse[1]> AOP$eSet$annotation > NULL > Browse > > Enter a frame number, or 0 to exit > > 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, > custom.contra > 2: annotation(AOP$eSet) > 3: function (classes, fdef, mtable) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> annotation(AOP$eSet) > Error during wrapup: unable to find an inherited method for function > "annotation", for signature "ExpressionSet" > Browse[1]> experimentData(AOP$eSet) > Experiment data > Experimenter name: > Laboratory: > Contact information: > Title: > URL: > PMIDs: > No abstract available. > Information is available on: preprocessing > notes: > : > > Browse[1]> sessionInfo() > R version 2.9.0 Under development (unstable) (2009-01-04 r47472) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE > = > en_US > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_US > .UTF > -8 > ;LC_COLLATE > = > en_US > .UTF > -8 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > en_US > .UTF > -8 > ;LC_PAPER > = > en_US > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] qvalue_1.17.0 limma_2.17.10 affyQCReport_1.21.1 > [4] geneplotter_1.21.2 lattice_0.17-20 annotate_1.21.4 > [7] RColorBrewer_1.0-2 affyPLM_1.19.7 preprocessCore_1.5.3 > [10] xtable_1.5-4 simpleaffy_2.19.3 gcrma_2.15.3 > [13] matchprobes_1.15.5 Biostrings_2.11.32 IRanges_1.1.40 > [16] genefilter_1.23.2 rat2302cdf_2.3.0 affycoretools_1.15.4 > [19] KEGG.db_2.2.5 GO.db_2.2.5 RSQLite_0.7-1 > [22] DBI_0.2-4 AnnotationDbi_1.5.16 affy_1.21.7 > [25] Biobase_2.3.10 graph_1.21.4 > > loaded via a namespace (and not attached): > [1] affyio_1.11.3 annaffy_1.15.0 biomaRt_1.99.5 > Category_2.9.11 > [5] cluster_1.11.12 GOstats_2.9.2 grid_2.9.0 > GSEABase_1.5.2 > [9] KernSmooth_2.22-22 RBGL_1.19.2 RCurl_0.94-1 > splines_2.9.0 > [13] survival_2.34-1 tools_2.9.0 XML_2.1-0 > Browse[1]> > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." > -- B. > F. Skinner > ****************************************************************** > > [[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

Hi Mark, This has been discussed already - it is worth searching the archives prior to posting. You can easily diagnose the problem by using: > find("annotation") [1] "package:IRanges" "package:Biobase" the problem is that both IRanges and Biobase define functions named IRanges and you must specify which one you want in your script (Biobase::annotation), or if it is in someone's package then they need to import the one they want by using a namespace. In general, one should not rely on a fortuitous ordering of the search list, nor too much on unique names for things - there are very few reserved words in R. Also, I don't think it is > ExpressionSet with $annotation equal to "rat2302". What's up? Mark these are likely to be S4 objects so the $ part is not correct. best wishes Robert On Mon, Feb 23, 2009 at 5:52 PM, Mark Kimpel <mwkimpel at="" gmail.com=""> wrote: > I have a function that has run well for several years and suddenly tonight > it blew up, unable to access the annotation slot of an ExpressionSet. Does > annotation(myExpressionSet) no longer work? > > Below is my output with my sessionInfo(). You will see that I am have an > ExpressionSet with $annotation equal to "rat2302". What's up? Mark > > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "annotation", for > signature "ExpressionSet" > > Enter a frame number, or 0 to exit > > 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, > custom.contra > 2: annotation(AOP$eSet) > 3: function (classes, fdef, mtable) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> attributes(AOP$eSet) > $.__classVersion__ > R Biobase eSet ExpressionSet > "2.9.0" "2.3.10" "1.1.0" "1.0.0" > > $assayData > <environment: 0x2ed74c80=""> > > $phenoData > An object of class "AnnotatedDataFrame" > sampleNames: BB02R001.CEL, BB02R002.CEL, ..., BB02R048.CEL (48 total) > varLabels and varMetadata description: > SampleNames: > Tube: > ...: ... > Lab.Hyb: NA > (11 total) > > $featureData > An object of class "AnnotatedDataFrame" > featureNames: 1367452_at, 1367453_at, ..., AFFX-TrpnX-M_at (31099 total) > varLabels and varMetadata description: none > > $experimentData > Experiment data > Experimenter name: > Laboratory: > Contact information: > Title: > URL: > PMIDs: > No abstract available. > Information is available on: preprocessing > notes: > : > > > $annotation > [1] "rat2302" > > $class > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" > > Browse[1]> AOP$eSet$annotation > NULL > Browse > > Enter a frame number, or 0 to exit > > 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, > custom.contra > 2: annotation(AOP$eSet) > 3: function (classes, fdef, mtable) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> annotation(AOP$eSet) > Error during wrapup: unable to find an inherited method for function > "annotation", for signature "ExpressionSet" > Browse[1]> experimentData(AOP$eSet) > Experiment data > Experimenter name: > Laboratory: > Contact information: > Title: > URL: > PMIDs: > No abstract available. > Information is available on: preprocessing > notes: > : > > Browse[1]> sessionInfo() > R version 2.9.0 Under development (unstable) (2009-01-04 r47472) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] tcltk stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] qvalue_1.17.0 limma_2.17.10 affyQCReport_1.21.1 > [4] geneplotter_1.21.2 lattice_0.17-20 annotate_1.21.4 > [7] RColorBrewer_1.0-2 affyPLM_1.19.7 preprocessCore_1.5.3 > [10] xtable_1.5-4 simpleaffy_2.19.3 gcrma_2.15.3 > [13] matchprobes_1.15.5 Biostrings_2.11.32 IRanges_1.1.40 > [16] genefilter_1.23.2 rat2302cdf_2.3.0 affycoretools_1.15.4 > [19] KEGG.db_2.2.5 GO.db_2.2.5 RSQLite_0.7-1 > [22] DBI_0.2-4 AnnotationDbi_1.5.16 affy_1.21.7 > [25] Biobase_2.3.10 graph_1.21.4 > > loaded via a namespace (and not attached): > [1] affyio_1.11.3 annaffy_1.15.0 biomaRt_1.99.5 > Category_2.9.11 > [5] cluster_1.11.12 GOstats_2.9.2 grid_2.9.0 > GSEABase_1.5.2 > [9] KernSmooth_2.22-22 RBGL_1.19.2 RCurl_0.94-1 > splines_2.9.0 > [13] survival_2.34-1 tools_2.9.0 XML_2.1-0 > Browse[1]> > ------------------------------------------------------------ > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 399-1219 Home > Skype: mkimpel > > "The real problem is not whether machines think but whether men do." -- B. > F. Skinner > ****************************************************************** > > [[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 > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hello All Can someone help me with unravelling a bit of confusion I have about the limma factorial design? 8.7 Factor Designs (Page 47 approx) in the user guide has three approaches that are basically equivalent. I am comparing the "sum to zero" and the "treatment contrast" approaches. In the sum to zero approach the comparisons are divided by 4 and this is where my misunderstanding lies. Just looking at the first gene as an example. I have put the expression values below to give an idea of the magnitudes. With the treatment contrast just extracting the coefficients straight I get the following (code below): eb$coef[1,] # Intercept dp TNF Interaction # 4.84942088 0.05031631 -0.36610669 0.15883329 With the sum to zero the comparisons are divided by 4. So one way to extract the coefficients is below in the code. Using this way (in effect multiplying by 4) I get the following: eb$coef[1,] # gm dp TNF Interaction # 18.9249361 -0.2594659 0.5733801 0.1588333 So here is my problem. The grand mean looks 4 times too large but the interaction matches the interaction from the treatments contrast approach. So I can have one "looking" right but not both. i.e. To multiply by 4 or not to multiply by 4, that is the question. How do I interpret this? What am I missing in my understanding? Thanks for any help Regards John # Sum to zero code fit<-lmFit(eset, design) contrast.matrix<-cbind(gm=c(4,0,0,0), dp=c(0,4,0,0), TNF=c(0,0,4,0), Interaction=c(0,0,0,4)) #contrast.matrix<-cbind(Interaction=c(0,0,-2,-2)) fit2<-contrasts.fit(fit, contrast.matrix) eb<-eBayes(fit2) # Treatment contrasts code design<-model.matrix(~dp*TNF) fit<-lmFit(eset, design) contrast.matrix<-cbind(Intercept=c(1, 0, 0, 0), dp=c(0,1,0,0), TNF=c(0,0,1,0), Interaction=c(0,0,0,1)) # Gene 1 expression level exprs1<-exprs[1,] # 4.865401 5.114202 4.719609 4.882969 4.857923 # 4.807370 4.538509 4.759865 4.779017 4.430844 # 4.519123 4.499975