Question: vennSelect error
0
gravatar for mali salmon
8.5 years ago by
mali salmon330
Israel
mali salmon330 wrote:
Dear list I am trying to use affycoretools for the analysis of affy yeast arrays. When I tried to use vennSelect in order generate HTML files containing the results of decideTests I got the following error: >annotation(eset)<-"yeast2.db" ... >fit2 <- eBayes(fit2) >results <- decideTests(fit2,lfc=1) >vennSelect(filtered,design,results,cont.matrix,fit2) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: cannot join using column gene_id - column not present in both tables) Any idea why I get this error? Thanks Mali > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 [22] limma_3.6.9 loaded via a namespace (and not attached): [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 [[alternative HTML version deleted]]
ADD COMMENTlink modified 8.5 years ago by James W. MacDonald52k • written 8.5 years ago by mali salmon330
Answer: vennSelect error
0
gravatar for James W. MacDonald
8.5 years ago by
United States
James W. MacDonald52k wrote:
Hi Mali, On 6/2/2011 7:40 AM, mali salmon wrote: > Dear list > I am trying to use affycoretools for the analysis of affy yeast arrays. > When I tried to use vennSelect in order generate HTML files containing the > results of decideTests I got the following error: > >> annotation(eset)<-"yeast2.db" Good thing you didn't snip the above line from your code. In the future, it is better to give us more than what you think we need, rather than less. The problem here is that you are resetting the annotation slot for your ExpressionSet (unnecessarily, and incorrectly). Not sure why you are doing this; did you see some code somewhere that lead you to believe this is either desired or necessary? If so, please tell us so we can hopefully get it corrected. Note that the annotation slot for an ExpressionSet doesn't imply annotation of (in this case) probeset IDs to genes, etc. The annotation slot contains name of the package that has the mappings of probes to probesets that were used to created the summarized values in that ExpressionSet. This is nice to have if you save the object, and wonder later how exactly the data were summarized. So start back at the line preceding the line above where you reset the annotation slot, and try again, without resetting the annotation slot. Best, Jim > ... >> fit2<- eBayes(fit2) >> results<- decideTests(fit2,lfc=1) >> vennSelect(filtered,design,results,cont.matrix,fit2) > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: cannot join using column gene_id - > column not present in both tables) > > Any idea why I get this error? > Thanks > Mali > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: i386-redhat-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 > [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 > [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 > [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 > [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 > [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 > [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 > [22] limma_3.6.9 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 > [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 > [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 > [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 > [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 > [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD COMMENTlink written 8.5 years ago by James W. MacDonald52k
Thanks Jim for your reply. I repeated the analysis without resetting the annotation slot but I still get the same error. Below is the code I used: >library(limma) >library(affy) >library(affycoretools) >data <- ReadAffy() >eset <- rma(data) >#remove low variance genes >library(genefilter) >eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >#remove control probes (AFFX) >filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >targets<-readTargets("targets.txt") >TS <- paste(targets$Strain, targets$Treatment, sep=".") >Strain <- factor(targets$Strain, levels=c("WT","Mu")) >Treatment <- factor(targets$Treatment, levels=c("U","S")) >design <- model.matrix(~Strain*Treatment) >fit <- lmFit(filtered, design) >cont.matrix <- cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >fit2 <- contrasts.fit(fit, cont.matrix) >fit2 <- eBayes(fit2) >results <- decideTests(fit2,lfc=1) >vennSelect(filtered, design, results, cont.matrix, fit2) Loading required package: yeast2.db Loading required package: org.Sc.sgd.db Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: cannot join using column gene_id - column not present in both tables) Thanks Mali On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Mali, > > > On 6/2/2011 7:40 AM, mali salmon wrote: > >> Dear list >> I am trying to use affycoretools for the analysis of affy yeast arrays. >> When I tried to use vennSelect in order generate HTML files containing the >> results of decideTests I got the following error: >> >> annotation(eset)<-"yeast2.db" >>> >> > Good thing you didn't snip the above line from your code. In the future, it > is better to give us more than what you think we need, rather than less. > > The problem here is that you are resetting the annotation slot for your > ExpressionSet (unnecessarily, and incorrectly). Not sure why you are doing > this; did you see some code somewhere that lead you to believe this is > either desired or necessary? If so, please tell us so we can hopefully get > it corrected. > > Note that the annotation slot for an ExpressionSet doesn't imply annotation > of (in this case) probeset IDs to genes, etc. The annotation slot contains > name of the package that has the mappings of probes to probesets that were > used to created the summarized values in that ExpressionSet. This is nice to > have if you save the object, and wonder later how exactly the data were > summarized. > > So start back at the line preceding the line above where you reset the > annotation slot, and try again, without resetting the annotation slot. > > Best, > > Jim > > > ... >> >>> fit2<- eBayes(fit2) >>> results<- decideTests(fit2,lfc=1) >>> vennSelect(filtered,design,results,cont.matrix,fit2) >>> >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (error in statement: cannot join using column gene_id - >> column not present in both tables) >> >> Any idea why I get this error? >> Thanks >> Mali >> >> sessionInfo() >>> >> R version 2.12.1 (2010-12-16) >> Platform: i386-redhat-linux-gnu (32-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >> [22] limma_3.6.9 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
ADD REPLYlink written 8.5 years ago by mali salmon330
Hi Mali, On 6/2/2011 3:00 PM, mali salmon wrote: > Thanks Jim for your reply. > I repeated the analysis without resetting the annotation slot but I still > get the same error. > Below is the code I used: > >> library(limma) >> library(affy) >> library(affycoretools) >> data<- ReadAffy() >> eset<- rma(data) >> #remove low variance genes >> library(genefilter) >> eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >> #remove control probes (AFFX) >> filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >> targets<-readTargets("targets.txt") >> TS<- paste(targets$Strain, targets$Treatment, sep=".") >> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >> Treatment<- factor(targets$Treatment, levels=c("U","S")) >> design<- model.matrix(~Strain*Treatment) >> fit<- lmFit(filtered, design) >> cont.matrix<- cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >> fit2<- contrasts.fit(fit, cont.matrix) >> fit2<- eBayes(fit2) >> results<- decideTests(fit2,lfc=1) >> vennSelect(filtered, design, results, cont.matrix, fit2) The problem is that you are by default trying to get annotation for > aaf.handler()[c(1:3,6:7, 9:12)] [1] "Probe" "Symbol" "Description" "GenBank" [5] "Gene" "UniGene" "PubMed" "Gene Ontology" [9] "Pathway" But since this is a yeast chip, not all of these are available. For this sort of issue I have included a '...' argument to vennSelect() that allows you to pass arguments to lower level functions, so you can just do something like library(annaffy) ## we need this to expose the aaf.handler() function vennSelect(filtered, design, results, cont.matrix, fit2, anncols = aaf.handler(chip = "yeast2.db")) Which will then give you all possible annotations for the yeast2.db chip, which are > aaf.handler(chip = "yeast2.db") [1] "Probe" "Description" "Chromosome" [4] "Chromosome Location" "PubMed" "Gene Ontology" [7] "Pathway" Unfortunately, you will still get the error you see, which comes from the call for Gene Ontology data, so if you amend to vennSelect(filtered, design, results, cont.matrix, fit2, anncols = aaf.handler(chip = "yeast2.db")[-6]) Then it will work. I will contact Colin Smith, the maintainer of annaffy, separately to see if he can track down the error you see with GO terms. Best, Jim > > Loading required package: yeast2.db > Loading required package: org.Sc.sgd.db > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: cannot join using column gene_id - > column not present in both tables) > > Thanks > Mali > > > > On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald<jmacdon at="" med.umich.edu="">wrote: > >> Hi Mali, >> >> >> On 6/2/2011 7:40 AM, mali salmon wrote: >> >>> Dear list >>> I am trying to use affycoretools for the analysis of affy yeast arrays. >>> When I tried to use vennSelect in order generate HTML files containing the >>> results of decideTests I got the following error: >>> >>> annotation(eset)<-"yeast2.db" >>>> >>> >> Good thing you didn't snip the above line from your code. In the future, it >> is better to give us more than what you think we need, rather than less. >> >> The problem here is that you are resetting the annotation slot for your >> ExpressionSet (unnecessarily, and incorrectly). Not sure why you are doing >> this; did you see some code somewhere that lead you to believe this is >> either desired or necessary? If so, please tell us so we can hopefully get >> it corrected. >> >> Note that the annotation slot for an ExpressionSet doesn't imply annotation >> of (in this case) probeset IDs to genes, etc. The annotation slot contains >> name of the package that has the mappings of probes to probesets that were >> used to created the summarized values in that ExpressionSet. This is nice to >> have if you save the object, and wonder later how exactly the data were >> summarized. >> >> So start back at the line preceding the line above where you reset the >> annotation slot, and try again, without resetting the annotation slot. >> >> Best, >> >> Jim >> >> >> ... >>> >>>> fit2<- eBayes(fit2) >>>> results<- decideTests(fit2,lfc=1) >>>> vennSelect(filtered,design,results,cont.matrix,fit2) >>>> >>> Error in sqliteExecStatement(con, statement, bind.data) : >>> RS-DBI driver: (error in statement: cannot join using column gene_id - >>> column not present in both tables) >>> >>> Any idea why I get this error? >>> Thanks >>> Mali >>> >>> sessionInfo() >>>> >>> R version 2.12.1 (2010-12-16) >>> Platform: i386-redhat-linux-gnu (32-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] grid stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >>> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >>> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >>> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >>> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >>> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>> [22] limma_3.6.9 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >>> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >>> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >>> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >>> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 8.5 years ago by James W. MacDonald52k
Thanks a lot Jim for your prompt support Mali On Thu, Jun 2, 2011 at 8:36 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Mali, > > > On 6/2/2011 3:00 PM, mali salmon wrote: > >> Thanks Jim for your reply. >> I repeated the analysis without resetting the annotation slot but I still >> get the same error. >> Below is the code I used: >> >> library(limma) >>> library(affy) >>> library(affycoretools) >>> data<- ReadAffy() >>> eset<- rma(data) >>> #remove low variance genes >>> library(genefilter) >>> eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >>> #remove control probes (AFFX) >>> filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >>> targets<-readTargets("targets.txt") >>> TS<- paste(targets$Strain, targets$Treatment, sep=".") >>> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >>> Treatment<- factor(targets$Treatment, levels=c("U","S")) >>> design<- model.matrix(~Strain*Treatment) >>> fit<- lmFit(filtered, design) >>> cont.matrix<- >>> cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >>> fit2<- contrasts.fit(fit, cont.matrix) >>> fit2<- eBayes(fit2) >>> results<- decideTests(fit2,lfc=1) >>> vennSelect(filtered, design, results, cont.matrix, fit2) >>> >> > The problem is that you are by default trying to get annotation for > > > aaf.handler()[c(1:3,6:7, 9:12)] > [1] "Probe" "Symbol" "Description" "GenBank" > [5] "Gene" "UniGene" "PubMed" "Gene Ontology" > [9] "Pathway" > > But since this is a yeast chip, not all of these are available. For this > sort of issue I have included a '...' argument to vennSelect() that allows > you to pass arguments to lower level functions, so you can just do something > like > > library(annaffy) ## we need this to expose the aaf.handler() function > vennSelect(filtered, design, results, cont.matrix, fit2, anncols = > aaf.handler(chip = "yeast2.db")) > > Which will then give you all possible annotations for the yeast2.db chip, > which are > > > aaf.handler(chip = "yeast2.db") > [1] "Probe" "Description" "Chromosome" > [4] "Chromosome Location" "PubMed" "Gene Ontology" > [7] "Pathway" > > Unfortunately, you will still get the error you see, which comes from the > call for Gene Ontology data, so if you amend to > > vennSelect(filtered, design, results, cont.matrix, fit2, anncols = > aaf.handler(chip = "yeast2.db")[-6]) > > Then it will work. I will contact Colin Smith, the maintainer of annaffy, > separately to see if he can track down the error you see with GO terms. > > Best, > > Jim > > > >> Loading required package: yeast2.db >> Loading required package: org.Sc.sgd.db >> Error in sqliteExecStatement(con, statement, bind.data) : >> RS-DBI driver: (error in statement: cannot join using column gene_id - >> column not present in both tables) >> >> Thanks >> Mali >> >> >> >> On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald<jmacdon@med.umich.edu>> >wrote: >> >> Hi Mali, >>> >>> >>> On 6/2/2011 7:40 AM, mali salmon wrote: >>> >>> Dear list >>>> I am trying to use affycoretools for the analysis of affy yeast arrays. >>>> When I tried to use vennSelect in order generate HTML files containing >>>> the >>>> results of decideTests I got the following error: >>>> >>>> annotation(eset)<-"yeast2.db" >>>> >>>>> >>>>> >>>> Good thing you didn't snip the above line from your code. In the >>> future, it >>> is better to give us more than what you think we need, rather than less. >>> >>> The problem here is that you are resetting the annotation slot for your >>> ExpressionSet (unnecessarily, and incorrectly). Not sure why you are >>> doing >>> this; did you see some code somewhere that lead you to believe this is >>> either desired or necessary? If so, please tell us so we can hopefully >>> get >>> it corrected. >>> >>> Note that the annotation slot for an ExpressionSet doesn't imply >>> annotation >>> of (in this case) probeset IDs to genes, etc. The annotation slot >>> contains >>> name of the package that has the mappings of probes to probesets that >>> were >>> used to created the summarized values in that ExpressionSet. This is nice >>> to >>> have if you save the object, and wonder later how exactly the data were >>> summarized. >>> >>> So start back at the line preceding the line above where you reset the >>> annotation slot, and try again, without resetting the annotation slot. >>> >>> Best, >>> >>> Jim >>> >>> >>> ... >>> >>>> >>>> fit2<- eBayes(fit2) >>>>> results<- decideTests(fit2,lfc=1) >>>>> vennSelect(filtered,design,results,cont.matrix,fit2) >>>>> >>>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>> RS-DBI driver: (error in statement: cannot join using column gene_id - >>>> column not present in both tables) >>>> >>>> Any idea why I get this error? >>>> Thanks >>>> Mali >>>> >>>> sessionInfo() >>>> >>>>> >>>>> R version 2.12.1 (2010-12-16) >>>> Platform: i386-redhat-linux-gnu (32-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] grid stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>>> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >>>> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >>>> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >>>> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >>>> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >>>> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>> [22] limma_3.6.9 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>>> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >>>> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >>>> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >>>> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >>>> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> >>> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
ADD REPLYlink written 8.5 years ago by mali salmon330
Dear Jim Thanks to your help I can generate HTML lists now, but the expression is missing for some of the samples. I also tried just to output lists of genes that are significant in each of the contrasts, and out of 10 samples, the expression of only 2-5 is printed (in both the txt and html files). Below is the function I used >limma2annaffy(filtered, fit2, design,cont.matrix, annotation(eset),adjust = "fdr",anncols = aaf.handler(chip="yeast2.db")[-c(5,6)], fldfilt=1,tstat=TRUE,pfilt = 0.05,text=TRUE,expression = TRUE) For "Diff" contrast genes only the expression of "Mu.S.1", "Mu.S.2" is printed For "Mu.SvsU" and "WT.SvsU" contrasts only the expression of "WT.S.1" "WT.S.2" "WT.S.3" "Mu.S.1" "Mu.S.2" is printed Below are the targets, contrast matrix and design objects >target FileName Strain Treatment 1 WT.U.1 WT U 2 WT.U.2 WT U 3 WT.U.3 WT U 4 WT.S.1 WT S 5 WT.S.2 WT S 6 WT.S.3 WT S 7 Mu.U.1 Mu U 8 Mu.U.2 Mu U 9 Mu.S.1 Mu S 10 Mu.S.2 Mu S > cont.matrix WT.SvsU Mu.SvsU Diff [1,] 0 0 0 [2,] 0 0 0 [3,] 1 1 0 [4,] 0 1 1 > design (Intercept) StrainMu TreatmentS StrainMu:TreatmentS 1 1 0 0 0 2 1 0 0 0 3 1 0 0 0 4 1 0 1 0 5 1 0 1 0 6 1 0 1 0 7 1 1 0 0 8 1 1 0 0 9 1 1 1 1 10 1 1 1 1 Thanks Mali On Fri, Jun 3, 2011 at 6:51 AM, mali salmon <shalmom1@gmail.com> wrote: > Thanks a lot Jim for your prompt support > Mali > > > On Thu, Jun 2, 2011 at 8:36 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > >> Hi Mali, >> >> >> On 6/2/2011 3:00 PM, mali salmon wrote: >> >>> Thanks Jim for your reply. >>> I repeated the analysis without resetting the annotation slot but I still >>> get the same error. >>> Below is the code I used: >>> >>> library(limma) >>>> library(affy) >>>> library(affycoretools) >>>> data<- ReadAffy() >>>> eset<- rma(data) >>>> #remove low variance genes >>>> library(genefilter) >>>> eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >>>> #remove control probes (AFFX) >>>> filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >>>> targets<-readTargets("targets.txt") >>>> TS<- paste(targets$Strain, targets$Treatment, sep=".") >>>> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >>>> Treatment<- factor(targets$Treatment, levels=c("U","S")) >>>> design<- model.matrix(~Strain*Treatment) >>>> fit<- lmFit(filtered, design) >>>> cont.matrix<- >>>> cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >>>> fit2<- contrasts.fit(fit, cont.matrix) >>>> fit2<- eBayes(fit2) >>>> results<- decideTests(fit2,lfc=1) >>>> vennSelect(filtered, design, results, cont.matrix, fit2) >>>> >>> >> The problem is that you are by default trying to get annotation for >> >> > aaf.handler()[c(1:3,6:7, 9:12)] >> [1] "Probe" "Symbol" "Description" "GenBank" >> [5] "Gene" "UniGene" "PubMed" "Gene Ontology" >> [9] "Pathway" >> >> But since this is a yeast chip, not all of these are available. For this >> sort of issue I have included a '...' argument to vennSelect() that allows >> you to pass arguments to lower level functions, so you can just do something >> like >> >> library(annaffy) ## we need this to expose the aaf.handler() function >> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >> aaf.handler(chip = "yeast2.db")) >> >> Which will then give you all possible annotations for the yeast2.db chip, >> which are >> >> > aaf.handler(chip = "yeast2.db") >> [1] "Probe" "Description" "Chromosome" >> [4] "Chromosome Location" "PubMed" "Gene Ontology" >> [7] "Pathway" >> >> Unfortunately, you will still get the error you see, which comes from the >> call for Gene Ontology data, so if you amend to >> >> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >> aaf.handler(chip = "yeast2.db")[-6]) >> >> Then it will work. I will contact Colin Smith, the maintainer of annaffy, >> separately to see if he can track down the error you see with GO terms. >> >> Best, >> >> Jim >> >> >> >>> Loading required package: yeast2.db >>> Loading required package: org.Sc.sgd.db >>> Error in sqliteExecStatement(con, statement, bind.data) : >>> RS-DBI driver: (error in statement: cannot join using column gene_id - >>> column not present in both tables) >>> >>> Thanks >>> Mali >>> >>> >>> >>> On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald<jmacdon@med.umich.edu>>> >wrote: >>> >>> Hi Mali, >>>> >>>> >>>> On 6/2/2011 7:40 AM, mali salmon wrote: >>>> >>>> Dear list >>>>> I am trying to use affycoretools for the analysis of affy yeast arrays. >>>>> When I tried to use vennSelect in order generate HTML files containing >>>>> the >>>>> results of decideTests I got the following error: >>>>> >>>>> annotation(eset)<-"yeast2.db" >>>>> >>>>>> >>>>>> >>>>> Good thing you didn't snip the above line from your code. In the >>>> future, it >>>> is better to give us more than what you think we need, rather than less. >>>> >>>> The problem here is that you are resetting the annotation slot for your >>>> ExpressionSet (unnecessarily, and incorrectly). Not sure why you are >>>> doing >>>> this; did you see some code somewhere that lead you to believe this is >>>> either desired or necessary? If so, please tell us so we can hopefully >>>> get >>>> it corrected. >>>> >>>> Note that the annotation slot for an ExpressionSet doesn't imply >>>> annotation >>>> of (in this case) probeset IDs to genes, etc. The annotation slot >>>> contains >>>> name of the package that has the mappings of probes to probesets that >>>> were >>>> used to created the summarized values in that ExpressionSet. This is >>>> nice to >>>> have if you save the object, and wonder later how exactly the data were >>>> summarized. >>>> >>>> So start back at the line preceding the line above where you reset the >>>> annotation slot, and try again, without resetting the annotation slot. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> ... >>>> >>>>> >>>>> fit2<- eBayes(fit2) >>>>>> results<- decideTests(fit2,lfc=1) >>>>>> vennSelect(filtered,design,results,cont.matrix,fit2) >>>>>> >>>>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>>> RS-DBI driver: (error in statement: cannot join using column gene_id >>>>> - >>>>> column not present in both tables) >>>>> >>>>> Any idea why I get this error? >>>>> Thanks >>>>> Mali >>>>> >>>>> sessionInfo() >>>>> >>>>>> >>>>>> R version 2.12.1 (2010-12-16) >>>>> Platform: i386-redhat-linux-gnu (32-bit) >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] grid stats graphics grDevices utils datasets methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>>>> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >>>>> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >>>>> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >>>>> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >>>>> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >>>>> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>> [22] limma_3.6.9 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>>>> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >>>>> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >>>>> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >>>>> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >>>>> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> Douglas Lab >>>> University of Michigan >>>> Department of Human Genetics >>>> 5912 Buhl >>>> 1241 E. Catherine St. >>>> Ann Arbor MI 48109-5618 >>>> 734-615-7826 >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and should not >>>> be >>>> used for urgent or sensitive issues >>>> >>>> >>> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not >> be used for urgent or sensitive issues >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 8.5 years ago by mali salmon330
OK, I have noticed that when I formulate the model in a different way, I get the expected results, and the expected columns are printed. The model that works fine is: >TS <- paste(targets$Strain, targets$Treatment, sep=".") >TS <- factor(TS, levels=c("WT.U","WT.S","Mu.U","Mu.S")) >design <- model.matrix(~0+TS) >colnames(design) <- levels(TS) >fit <- lmFit(filtered, design) >cont.matrix <- makeContrasts(WT.SvsU=WT.S-WT.U, Mu.SvsU=Mu.S-Mu.U, Diff=(Mu.S-Mu.U)-(WT.S-WT.U),levels=design) >fit2 <- contrasts.fit(fit, cont.matrix) >fit2 <- eBayes(fit2) Then when I run "limma2annaffy" I get the correct columns. However, when I use a different approach (but equivalent according to the user guide) below, the wrong columns are printed when I use "limma2annaffy": >Strain <- factor(targets$Strain, levels=c("WT","Mu")) >Treatment <- factor(targets$Treatment, levels=c("U","S")) >design <- model.matrix(~Strain*Treatment) >fit <- lmFit(filtered, design) >cont.matrix <- cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >fit2 <- contrasts.fit(fit, cont.matrix) >fit2 <- eBayes(fit2) Any idea what I did wrong? Thank Mali On Sun, Jun 5, 2011 at 8:54 AM, mali salmon <shalmom1@gmail.com> wrote: > Dear Jim > Thanks to your help I can generate HTML lists now, but the expression is > missing for some of the samples. > I also tried just to output lists of genes that are significant in each of > the contrasts, and out of 10 samples, the expression of only 2-5 is printed > (in both the txt and html files). > Below is the function I used > >limma2annaffy(filtered, fit2, design,cont.matrix, annotation(eset),adjust > = "fdr",anncols = aaf.handler(chip="yeast2.db")[-c(5,6)], > fldfilt=1,tstat=TRUE,pfilt = 0.05,text=TRUE,expression = TRUE) > > For "Diff" contrast genes only the expression of "Mu.S.1", "Mu.S.2" is > printed > For "Mu.SvsU" and "WT.SvsU" contrasts only the expression of "WT.S.1" > "WT.S.2" "WT.S.3" "Mu.S.1" "Mu.S.2" is printed > > Below are the targets, contrast matrix and design objects > > >target > FileName Strain Treatment > 1 WT.U.1 WT U > 2 WT.U.2 WT U > 3 WT.U.3 WT U > 4 WT.S.1 WT S > 5 WT.S.2 WT S > 6 WT.S.3 WT S > 7 Mu.U.1 Mu U > 8 Mu.U.2 Mu U > 9 Mu.S.1 Mu S > 10 Mu.S.2 Mu S > > > > cont.matrix > WT.SvsU Mu.SvsU Diff > [1,] 0 0 0 > [2,] 0 0 0 > [3,] 1 1 0 > [4,] 0 1 1 > > > design > (Intercept) StrainMu TreatmentS StrainMu:TreatmentS > 1 1 0 0 0 > 2 1 0 0 0 > 3 1 0 0 0 > 4 1 0 1 0 > 5 1 0 1 0 > 6 1 0 1 0 > 7 1 1 0 0 > 8 1 1 0 0 > 9 1 1 1 1 > 10 1 1 1 1 > > Thanks > Mali > > > > > > On Fri, Jun 3, 2011 at 6:51 AM, mali salmon <shalmom1@gmail.com> wrote: > >> Thanks a lot Jim for your prompt support >> Mali >> >> >> On Thu, Jun 2, 2011 at 8:36 PM, James W. MacDonald <jmacdon@med.umich.edu>> > wrote: >> >>> Hi Mali, >>> >>> >>> On 6/2/2011 3:00 PM, mali salmon wrote: >>> >>>> Thanks Jim for your reply. >>>> I repeated the analysis without resetting the annotation slot but I >>>> still >>>> get the same error. >>>> Below is the code I used: >>>> >>>> library(limma) >>>>> library(affy) >>>>> library(affycoretools) >>>>> data<- ReadAffy() >>>>> eset<- rma(data) >>>>> #remove low variance genes >>>>> library(genefilter) >>>>> eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >>>>> #remove control probes (AFFX) >>>>> filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >>>>> targets<-readTargets("targets.txt") >>>>> TS<- paste(targets$Strain, targets$Treatment, sep=".") >>>>> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >>>>> Treatment<- factor(targets$Treatment, levels=c("U","S")) >>>>> design<- model.matrix(~Strain*Treatment) >>>>> fit<- lmFit(filtered, design) >>>>> cont.matrix<- >>>>> cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >>>>> fit2<- contrasts.fit(fit, cont.matrix) >>>>> fit2<- eBayes(fit2) >>>>> results<- decideTests(fit2,lfc=1) >>>>> vennSelect(filtered, design, results, cont.matrix, fit2) >>>>> >>>> >>> The problem is that you are by default trying to get annotation for >>> >>> > aaf.handler()[c(1:3,6:7, 9:12)] >>> [1] "Probe" "Symbol" "Description" "GenBank" >>> [5] "Gene" "UniGene" "PubMed" "Gene Ontology" >>> [9] "Pathway" >>> >>> But since this is a yeast chip, not all of these are available. For this >>> sort of issue I have included a '...' argument to vennSelect() that allows >>> you to pass arguments to lower level functions, so you can just do something >>> like >>> >>> library(annaffy) ## we need this to expose the aaf.handler() function >>> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >>> aaf.handler(chip = "yeast2.db")) >>> >>> Which will then give you all possible annotations for the yeast2.db chip, >>> which are >>> >>> > aaf.handler(chip = "yeast2.db") >>> [1] "Probe" "Description" "Chromosome" >>> [4] "Chromosome Location" "PubMed" "Gene Ontology" >>> [7] "Pathway" >>> >>> Unfortunately, you will still get the error you see, which comes from the >>> call for Gene Ontology data, so if you amend to >>> >>> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >>> aaf.handler(chip = "yeast2.db")[-6]) >>> >>> Then it will work. I will contact Colin Smith, the maintainer of annaffy, >>> separately to see if he can track down the error you see with GO terms. >>> >>> Best, >>> >>> Jim >>> >>> >>> >>>> Loading required package: yeast2.db >>>> Loading required package: org.Sc.sgd.db >>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>> RS-DBI driver: (error in statement: cannot join using column gene_id - >>>> column not present in both tables) >>>> >>>> Thanks >>>> Mali >>>> >>>> >>>> >>>> On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald< >>>> jmacdon@med.umich.edu>wrote: >>>> >>>> Hi Mali, >>>>> >>>>> >>>>> On 6/2/2011 7:40 AM, mali salmon wrote: >>>>> >>>>> Dear list >>>>>> I am trying to use affycoretools for the analysis of affy yeast >>>>>> arrays. >>>>>> When I tried to use vennSelect in order generate HTML files containing >>>>>> the >>>>>> results of decideTests I got the following error: >>>>>> >>>>>> annotation(eset)<-"yeast2.db" >>>>>> >>>>>>> >>>>>>> >>>>>> Good thing you didn't snip the above line from your code. In the >>>>> future, it >>>>> is better to give us more than what you think we need, rather than >>>>> less. >>>>> >>>>> The problem here is that you are resetting the annotation slot for your >>>>> ExpressionSet (unnecessarily, and incorrectly). Not sure why you are >>>>> doing >>>>> this; did you see some code somewhere that lead you to believe this is >>>>> either desired or necessary? If so, please tell us so we can hopefully >>>>> get >>>>> it corrected. >>>>> >>>>> Note that the annotation slot for an ExpressionSet doesn't imply >>>>> annotation >>>>> of (in this case) probeset IDs to genes, etc. The annotation slot >>>>> contains >>>>> name of the package that has the mappings of probes to probesets that >>>>> were >>>>> used to created the summarized values in that ExpressionSet. This is >>>>> nice to >>>>> have if you save the object, and wonder later how exactly the data were >>>>> summarized. >>>>> >>>>> So start back at the line preceding the line above where you reset the >>>>> annotation slot, and try again, without resetting the annotation slot. >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> ... >>>>> >>>>>> >>>>>> fit2<- eBayes(fit2) >>>>>>> results<- decideTests(fit2,lfc=1) >>>>>>> vennSelect(filtered,design,results,cont.matrix,fit2) >>>>>>> >>>>>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>>>> RS-DBI driver: (error in statement: cannot join using column gene_id >>>>>> - >>>>>> column not present in both tables) >>>>>> >>>>>> Any idea why I get this error? >>>>>> Thanks >>>>>> Mali >>>>>> >>>>>> sessionInfo() >>>>>> >>>>>>> >>>>>>> R version 2.12.1 (2010-12-16) >>>>>> Platform: i386-redhat-linux-gnu (32-bit) >>>>>> >>>>>> locale: >>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>> >>>>>> attached base packages: >>>>>> [1] grid stats graphics grDevices utils datasets >>>>>> methods >>>>>> [8] base >>>>>> >>>>>> other attached packages: >>>>>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>>>>> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >>>>>> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >>>>>> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >>>>>> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >>>>>> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >>>>>> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>>> [22] limma_3.6.9 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>>>>> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >>>>>> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >>>>>> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >>>>>> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >>>>>> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor@r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> Douglas Lab >>>>> University of Michigan >>>>> Department of Human Genetics >>>>> 5912 Buhl >>>>> 1241 E. Catherine St. >>>>> Ann Arbor MI 48109-5618 >>>>> 734-615-7826 >>>>> ********************************************************** >>>>> Electronic Mail is not secure, may not be read every day, and should >>>>> not be >>>>> used for urgent or sensitive issues >>>>> >>>>> >>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be used for urgent or sensitive issues >>> >> >> > [[alternative HTML version deleted]]
ADD REPLYlink written 8.5 years ago by mali salmon330
Hi Mali, On 6/5/2011 2:36 AM, mali salmon wrote: > OK, I have noticed that when I formulate the model in a different way, I get > the expected results, and the expected columns are printed. > The model that works fine is: > >> TS<- paste(targets$Strain, targets$Treatment, sep=".") >> TS<- factor(TS, levels=c("WT.U","WT.S","Mu.U","Mu.S")) >> design<- model.matrix(~0+TS) >> colnames(design)<- levels(TS) >> fit<- lmFit(filtered, design) >> cont.matrix<- makeContrasts(WT.SvsU=WT.S-WT.U, Mu.SvsU=Mu.S-Mu.U, > Diff=(Mu.S-Mu.U)-(WT.S-WT.U),levels=design) >> fit2<- contrasts.fit(fit, cont.matrix) >> fit2<- eBayes(fit2) > > Then when I run "limma2annaffy" I get the correct columns. > > However, when I use a different approach (but equivalent according to the > user guide) below, the wrong columns are printed when I use > "limma2annaffy": >> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >> Treatment<- factor(targets$Treatment, levels=c("U","S")) >> design<- model.matrix(~Strain*Treatment) >> fit<- lmFit(filtered, design) >> cont.matrix<- cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >> fit2<- contrasts.fit(fit, cont.matrix) >> fit2<- eBayes(fit2) > > Any idea what I did wrong? You didn't do anything wrong per se, if anything it is a shortcoming of limma2annaffy(). In order to make the code simpler, I require that the model be specified using a cell means model (as you did above where it worked for you), rather than a factor effects model (the parameterization you tried that didn't work). Maybe this isn't stated as explicitly as it should be. I'll take a look at the documentation and see if I can make some changes. Best, Jim > Thank > Mali > > > On Sun, Jun 5, 2011 at 8:54 AM, mali salmon<shalmom1 at="" gmail.com=""> wrote: > >> Dear Jim >> Thanks to your help I can generate HTML lists now, but the expression is >> missing for some of the samples. >> I also tried just to output lists of genes that are significant in each of >> the contrasts, and out of 10 samples, the expression of only 2-5 is printed >> (in both the txt and html files). >> Below is the function I used >>> limma2annaffy(filtered, fit2, design,cont.matrix, annotation(eset),adjust >> = "fdr",anncols = aaf.handler(chip="yeast2.db")[-c(5,6)], >> fldfilt=1,tstat=TRUE,pfilt = 0.05,text=TRUE,expression = TRUE) >> >> For "Diff" contrast genes only the expression of "Mu.S.1", "Mu.S.2" is >> printed >> For "Mu.SvsU" and "WT.SvsU" contrasts only the expression of "WT.S.1" >> "WT.S.2" "WT.S.3" "Mu.S.1" "Mu.S.2" is printed >> >> Below are the targets, contrast matrix and design objects >> >>> target >> FileName Strain Treatment >> 1 WT.U.1 WT U >> 2 WT.U.2 WT U >> 3 WT.U.3 WT U >> 4 WT.S.1 WT S >> 5 WT.S.2 WT S >> 6 WT.S.3 WT S >> 7 Mu.U.1 Mu U >> 8 Mu.U.2 Mu U >> 9 Mu.S.1 Mu S >> 10 Mu.S.2 Mu S >> >> >>> cont.matrix >> WT.SvsU Mu.SvsU Diff >> [1,] 0 0 0 >> [2,] 0 0 0 >> [3,] 1 1 0 >> [4,] 0 1 1 >> >>> design >> (Intercept) StrainMu TreatmentS StrainMu:TreatmentS >> 1 1 0 0 0 >> 2 1 0 0 0 >> 3 1 0 0 0 >> 4 1 0 1 0 >> 5 1 0 1 0 >> 6 1 0 1 0 >> 7 1 1 0 0 >> 8 1 1 0 0 >> 9 1 1 1 1 >> 10 1 1 1 1 >> >> Thanks >> Mali >> >> >> >> >> >> On Fri, Jun 3, 2011 at 6:51 AM, mali salmon<shalmom1 at="" gmail.com=""> wrote: >> >>> Thanks a lot Jim for your prompt support >>> Mali >>> >>> >>> On Thu, Jun 2, 2011 at 8:36 PM, James W. MacDonald<jmacdon at="" med.umich.edu="">>>> wrote: >>> >>>> Hi Mali, >>>> >>>> >>>> On 6/2/2011 3:00 PM, mali salmon wrote: >>>> >>>>> Thanks Jim for your reply. >>>>> I repeated the analysis without resetting the annotation slot but I >>>>> still >>>>> get the same error. >>>>> Below is the code I used: >>>>> >>>>> library(limma) >>>>>> library(affy) >>>>>> library(affycoretools) >>>>>> data<- ReadAffy() >>>>>> eset<- rma(data) >>>>>> #remove low variance genes >>>>>> library(genefilter) >>>>>> eset2<-varFilter(eset,var.func=IQR,var.cutoff=0.1) >>>>>> #remove control probes (AFFX) >>>>>> filtered<-featureFilter(eset2, require.entrez=F, remove.dupEntrez=F) >>>>>> targets<-readTargets("targets.txt") >>>>>> TS<- paste(targets$Strain, targets$Treatment, sep=".") >>>>>> Strain<- factor(targets$Strain, levels=c("WT","Mu")) >>>>>> Treatment<- factor(targets$Treatment, levels=c("U","S")) >>>>>> design<- model.matrix(~Strain*Treatment) >>>>>> fit<- lmFit(filtered, design) >>>>>> cont.matrix<- >>>>>> cbind(WT.SvsU=c(0,0,1,0),Mu.SvsU=c(0,0,1,1),Diff=c(0,0,0,1)) >>>>>> fit2<- contrasts.fit(fit, cont.matrix) >>>>>> fit2<- eBayes(fit2) >>>>>> results<- decideTests(fit2,lfc=1) >>>>>> vennSelect(filtered, design, results, cont.matrix, fit2) >>>>>> >>>>> >>>> The problem is that you are by default trying to get annotation for >>>> >>>>> aaf.handler()[c(1:3,6:7, 9:12)] >>>> [1] "Probe" "Symbol" "Description" "GenBank" >>>> [5] "Gene" "UniGene" "PubMed" "Gene Ontology" >>>> [9] "Pathway" >>>> >>>> But since this is a yeast chip, not all of these are available. For this >>>> sort of issue I have included a '...' argument to vennSelect() that allows >>>> you to pass arguments to lower level functions, so you can just do something >>>> like >>>> >>>> library(annaffy) ## we need this to expose the aaf.handler() function >>>> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >>>> aaf.handler(chip = "yeast2.db")) >>>> >>>> Which will then give you all possible annotations for the yeast2.db chip, >>>> which are >>>> >>>>> aaf.handler(chip = "yeast2.db") >>>> [1] "Probe" "Description" "Chromosome" >>>> [4] "Chromosome Location" "PubMed" "Gene Ontology" >>>> [7] "Pathway" >>>> >>>> Unfortunately, you will still get the error you see, which comes from the >>>> call for Gene Ontology data, so if you amend to >>>> >>>> vennSelect(filtered, design, results, cont.matrix, fit2, anncols = >>>> aaf.handler(chip = "yeast2.db")[-6]) >>>> >>>> Then it will work. I will contact Colin Smith, the maintainer of annaffy, >>>> separately to see if he can track down the error you see with GO terms. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>>> Loading required package: yeast2.db >>>>> Loading required package: org.Sc.sgd.db >>>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>>> RS-DBI driver: (error in statement: cannot join using column gene_id - >>>>> column not present in both tables) >>>>> >>>>> Thanks >>>>> Mali >>>>> >>>>> >>>>> >>>>> On Thu, Jun 2, 2011 at 2:45 PM, James W. MacDonald< >>>>> jmacdon at med.umich.edu>wrote: >>>>> >>>>> Hi Mali, >>>>>> >>>>>> >>>>>> On 6/2/2011 7:40 AM, mali salmon wrote: >>>>>> >>>>>> Dear list >>>>>>> I am trying to use affycoretools for the analysis of affy yeast >>>>>>> arrays. >>>>>>> When I tried to use vennSelect in order generate HTML files containing >>>>>>> the >>>>>>> results of decideTests I got the following error: >>>>>>> >>>>>>> annotation(eset)<-"yeast2.db" >>>>>>> >>>>>>>> >>>>>>>> >>>>>>> Good thing you didn't snip the above line from your code. In the >>>>>> future, it >>>>>> is better to give us more than what you think we need, rather than >>>>>> less. >>>>>> >>>>>> The problem here is that you are resetting the annotation slot for your >>>>>> ExpressionSet (unnecessarily, and incorrectly). Not sure why you are >>>>>> doing >>>>>> this; did you see some code somewhere that lead you to believe this is >>>>>> either desired or necessary? If so, please tell us so we can hopefully >>>>>> get >>>>>> it corrected. >>>>>> >>>>>> Note that the annotation slot for an ExpressionSet doesn't imply >>>>>> annotation >>>>>> of (in this case) probeset IDs to genes, etc. The annotation slot >>>>>> contains >>>>>> name of the package that has the mappings of probes to probesets that >>>>>> were >>>>>> used to created the summarized values in that ExpressionSet. This is >>>>>> nice to >>>>>> have if you save the object, and wonder later how exactly the data were >>>>>> summarized. >>>>>> >>>>>> So start back at the line preceding the line above where you reset the >>>>>> annotation slot, and try again, without resetting the annotation slot. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jim >>>>>> >>>>>> >>>>>> ... >>>>>> >>>>>>> >>>>>>> fit2<- eBayes(fit2) >>>>>>>> results<- decideTests(fit2,lfc=1) >>>>>>>> vennSelect(filtered,design,results,cont.matrix,fit2) >>>>>>>> >>>>>>>> Error in sqliteExecStatement(con, statement, bind.data) : >>>>>>> RS-DBI driver: (error in statement: cannot join using column gene_id >>>>>>> - >>>>>>> column not present in both tables) >>>>>>> >>>>>>> Any idea why I get this error? >>>>>>> Thanks >>>>>>> Mali >>>>>>> >>>>>>> sessionInfo() >>>>>>> >>>>>>>> >>>>>>>> R version 2.12.1 (2010-12-16) >>>>>>> Platform: i386-redhat-linux-gnu (32-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] grid stats graphics grDevices utils datasets >>>>>>> methods >>>>>>> [8] base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] hgu133a2.db_2.4.5 org.Hs.eg.db_2.4.6 annaffy_1.22.0 >>>>>>> [4] affycoretools_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 >>>>>>> [7] gplots_2.8.0 caTools_1.11 bitops_1.0-4.1 >>>>>>> [10] gdata_2.8.1 gtools_2.6.2 yeast2.db_2.4.5 >>>>>>> [13] org.Sc.sgd.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 >>>>>>> [16] annotate_1.28.1 AnnotationDbi_1.12.0 genefilter_1.32.0 >>>>>>> [19] yeast2cdf_2.7.0 affy_1.28.0 Biobase_2.10.0 >>>>>>> [22] limma_3.6.9 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] affyio_1.18.0 biomaRt_2.6.0 Biostrings_2.18.2 >>>>>>> [4] Category_2.16.1 gcrma_2.22.0 GOstats_2.16.0 >>>>>>> [7] graph_1.28.0 GSEABase_1.12.2 IRanges_1.8.9 >>>>>>> [10] preprocessCore_1.12.0 RBGL_1.26.0 RCurl_1.5-0 >>>>>>> [13] splines_2.12.1 survival_2.36-2 tcltk_2.12.1 >>>>>>> [16] tools_2.12.1 XML_3.2-0 xtable_1.5-6 >>>>>>> >>>>>>> [[alternative HTML version deleted]] >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>> -- >>>>>> James W. MacDonald, M.S. >>>>>> Biostatistician >>>>>> Douglas Lab >>>>>> University of Michigan >>>>>> Department of Human Genetics >>>>>> 5912 Buhl >>>>>> 1241 E. Catherine St. >>>>>> Ann Arbor MI 48109-5618 >>>>>> 734-615-7826 >>>>>> ********************************************************** >>>>>> Electronic Mail is not secure, may not be read every day, and should >>>>>> not be >>>>>> used for urgent or sensitive issues >>>>>> >>>>>> >>>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> Douglas Lab >>>> University of Michigan >>>> Department of Human Genetics >>>> 5912 Buhl >>>> 1241 E. Catherine St. >>>> Ann Arbor MI 48109-5618 >>>> 734-615-7826 >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and should not >>>> be used for urgent or sensitive issues >>>> >>> >>> >> > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
ADD REPLYlink written 8.5 years ago by James W. MacDonald52k
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