Hi, I asked this question some weeks ago, but I couldn't solve the problem yet. I would be very glad if somebody could help me.. I tried to use pairwise.comparison in simpleaffy to get a table of results, but there is an error with the annotation... Thanks for your help, Marietta Herrmann > data<-ReadAffy() > pData<-data.frame(genotype=c(1,1,1,2,2,2), replicate=c(1,2,3,1,2,3)) > rownames(pData)<-sampleNames(data) > vl<-data.frame(c("1 is B6, 2 is D2", "arbitrary numbering")) > phenoData(data)<-new("AnnotatedDataFrame", data=pData, varMetadata=vl) > library(gcrma) > eset<-gcrma(data) > library(simpleaffy) > results <- pairwise.comparison(eset, "genotype", spots=data) > significant<-pairwise.filter(results, fc=log2(2), tt=0.05, present.by.group=T) [1] "Checking member 1 in group: ' genotype '" [1] "Checking member 2 in group: ' genotype '" > summary <- results.summary(significant, "mouse4302") Error in library(cdfname, character.only = TRUE) : there is no package called 'mouse4302' > summary <- results.summary(significant, "mouse4302.db") Loading required package: AnnotationDbi Loading required package: DBI Error in get(paste(cdfname, "SYMBOL", sep = "")) : variable "mouse4302.dbSYMBOL" was not found > sessionInfo() R version 2.8.0 (2008-10-20) i386-apple-darwin9.5.0 locale: de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] mouse4302.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [4] AnnotationDbi_1.4.1 simpleaffy_2.18.0 genefilter_1.22.0 [7] survival_2.34-1 mouse4302probe_2.3.0 mouse4302cdf_2.3.0 [10] gcrma_2.14.1 matchprobes_1.14.0 affy_1.20.0 [13] Biobase_2.2.1 loaded via a namespace (and not attached): [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0

Hi Marietta, This appears to be a bug in simpleaffy due to not upgrading to accept the new annotation package names. You might try contacting the maintainer directly, as he may have missed your questions to the list. Best, Jim Marietta Herrmann wrote: > Hi, > > I asked this question some weeks ago, but I couldn't solve the problem yet. > I would be very glad if somebody could help me.. > > I tried to use pairwise.comparison in simpleaffy to get a table of results, > but there is an error with the annotation... > > Thanks for your help, > > Marietta Herrmann > > > >> data<-ReadAffy() >> pData<-data.frame(genotype=c(1,1,1,2,2,2), replicate=c(1,2,3,1,2,3)) >> rownames(pData)<-sampleNames(data) >> vl<-data.frame(c("1 is B6, 2 is D2", "arbitrary numbering")) >> phenoData(data)<-new("AnnotatedDataFrame", data=pData, varMetadata=vl) >> library(gcrma) >> eset<-gcrma(data) >> library(simpleaffy) >> results <- pairwise.comparison(eset, "genotype", spots=data) >> significant<-pairwise.filter(results, fc=log2(2), tt=0.05, present.by.group=T) > [1] "Checking member 1 in group: ' genotype '" > [1] "Checking member 2 in group: ' genotype '" > >> summary <- results.summary(significant, "mouse4302") > Error in library(cdfname, character.only = TRUE) : > there is no package called 'mouse4302' > >> summary <- results.summary(significant, "mouse4302.db") > Loading required package: AnnotationDbi > Loading required package: DBI > Error in get(paste(cdfname, "SYMBOL", sep = "")) : > variable "mouse4302.dbSYMBOL" was not found > >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin9.5.0 > > locale: > de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] mouse4302.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 > [4] AnnotationDbi_1.4.1 simpleaffy_2.18.0 genefilter_1.22.0 > [7] survival_2.34-1 mouse4302probe_2.3.0 mouse4302cdf_2.3.0 > [10] gcrma_2.14.1 matchprobes_1.14.0 affy_1.20.0 > [13] Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

Hi Marietta, This appears to be a bug in simpleaffy due to not upgrading to accept the new annotation package names. You might try contacting the maintainer directly, as he may have missed your questions to the list. Best, Jim Marietta Herrmann wrote: > Hi, > > I asked this question some weeks ago, but I couldn't solve the problem yet. > I would be very glad if somebody could help me.. > > I tried to use pairwise.comparison in simpleaffy to get a table of results, > but there is an error with the annotation... > > Thanks for your help, > > Marietta Herrmann > > > >> data<-ReadAffy() >> pData<-data.frame(genotype=c(1,1,1,2,2,2), replicate=c(1,2,3,1,2,3)) >> rownames(pData)<-sampleNames(data) >> vl<-data.frame(c("1 is B6, 2 is D2", "arbitrary numbering")) >> phenoData(data)<-new("AnnotatedDataFrame", data=pData, varMetadata=vl) >> library(gcrma) >> eset<-gcrma(data) >> library(simpleaffy) >> results <- pairwise.comparison(eset, "genotype", spots=data) >> significant<-pairwise.filter(results, fc=log2(2), tt=0.05, present.by.group=T) > [1] "Checking member 1 in group: ' genotype '" > [1] "Checking member 2 in group: ' genotype '" > >> summary <- results.summary(significant, "mouse4302") > Error in library(cdfname, character.only = TRUE) : > there is no package called 'mouse4302' > >> summary <- results.summary(significant, "mouse4302.db") > Loading required package: AnnotationDbi > Loading required package: DBI > Error in get(paste(cdfname, "SYMBOL", sep = "")) : > variable "mouse4302.dbSYMBOL" was not found > >> sessionInfo() > R version 2.8.0 (2008-10-20) > i386-apple-darwin9.5.0 > > locale: > de_DE.UTF-8/de_DE.UTF-8/C/C/de_DE.UTF-8/C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] mouse4302.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 > [4] AnnotationDbi_1.4.1 simpleaffy_2.18.0 genefilter_1.22.0 > [7] survival_2.34-1 mouse4302probe_2.3.0 mouse4302cdf_2.3.0 > [10] gcrma_2.14.1 matchprobes_1.14.0 affy_1.20.0 > [13] Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 preprocessCore_1.4.0 > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662