Thanks a lot Jim for your prompt support Mali On Thu, Jun 2, 2011 at 8:36 PM, James W. MacDonald 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> >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]]