hii... this is Deepak.... i am working on analysis of microarray data. We tried using this code snippet phenoData(spikein95) <- new("phenoData", pData = pd, varLabels = vl) but it said that phenoData is now defunct and we need to use AnnotatedDataFrame. And i am not able to proceed because of the following error AnnotatedDataFrame(x1)<-new("AnnotatedDataFrame",pData=pd, varLabels=v1) Error in .nextMethod(.Object, ...) : invalid names for slots of class “AnnotatedDataFrame”: pData, varLabels i am basically trying to segregate the samples into 3 parts containing normal, HSIL and SCC data and this is the code that i have used till now... setwd("E:\\Project\\CEL files\\Old\\GSE7803-3") > f1=list.celfiles(path="E:\\Project\\CEL files\\Old\\GSE7803-3") > x1<-ReadAffy(filenames=f1) > pd <- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2, + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3), + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,4,5,6,7, + 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21)) > rownames(pd) <- sampleNames(x1) > v1 <- list(population = "1 is normal, 2 is HSIL, 3 is SCC", replicate="arbitary numbering") i further wish to perform rma and then generate a MA plot. kindly help me rectify this error and if possible explain with an example so that i could proceed further. [[alternative HTML version deleted]]

Hi Deepak, you need to construct an AnnotatedDataFrame in the following way: AnnotatedDataFrame(data=df, varMetaData=metaData) Look-up the help page which is well documented: help("AnnotatedDataFrame") HTH. J. On 02/03/12 10:11, Deepak Datta wrote: > hii... this is Deepak.... > > i am working on analysis of microarray data. > > We tried using this code snippet > phenoData(spikein95)<- new("phenoData", pData = pd, varLabels = vl) > > but it said that phenoData is now defunct and we need to use > AnnotatedDataFrame. And i am not able to proceed because of the following > error > > AnnotatedDataFrame(x1)<-new("AnnotatedDataFrame",pData=pd, varLabels=v1) > Error in .nextMethod(.Object, ...) : > invalid names for slots of class ?AnnotatedDataFrame?: pData, varLabels > > > i am basically trying to segregate the samples into 3 parts containing > normal, HSIL and SCC data and this is the code that i have used till now... > > setwd("E:\\Project\\CEL files\\Old\\GSE7803-3") >> f1=list.celfiles(path="E:\\Project\\CEL files\\Old\\GSE7803-3") >> x1<-ReadAffy(filenames=f1) >> pd<- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2, > + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3), > + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,4,5,6,7, > + 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21)) >> rownames(pd)<- sampleNames(x1) >> v1<- list(population = "1 is normal, 2 is HSIL, 3 is SCC", > replicate="arbitary numbering") > > > i further wish to perform rma and then generate a MA plot. > > kindly help me rectify this error and if possible explain with an example > so that i could proceed further. > > [[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

Hi Deepak, please keep the thread on the list for other users. On 02/03/12 10:28, Deepak Datta wrote: > hey James, i have read the help page and i did not find it helpful. i > would really appreciate if you could please explain me with an example > giving details on creating a metaData something like this should work: new("AnnotatedDataFrame", data=pd, varMetadata=data.frame(labelDescription=unlist(v1))) since your v1 is a list (it needen't be). Best. J. > > > On Fri, Mar 2, 2012 at 3:49 PM, James F. Reid > <james.reid at="" ifom-ieo-campus.it="" <mailto:james.reid="" at="" ifom-ieo-="" campus.it="">> > wrote: > > Hi Deepak, > > you need to construct an AnnotatedDataFrame in the following way: > AnnotatedDataFrame(data=df, varMetaData=metaData) > Look-up the help page which is well documented: > help("AnnotatedDataFrame") > > HTH. > J. > > > On 02/03/12 10:11, Deepak Datta wrote: > > hii... this is Deepak.... > > i am working on analysis of microarray data. > > We tried using this code snippet > phenoData(spikein95)<- new("phenoData", pData = pd, varLabels = vl) > > but it said that phenoData is now defunct and we need to use > AnnotatedDataFrame. And i am not able to proceed because of the > following > error > > AnnotatedDataFrame(x1)<-new("__AnnotatedDataFrame",pData=pd, > varLabels=v1) > Error in .nextMethod(.Object, ...) : > invalid names for slots of class ?AnnotatedDataFrame?: pData, > varLabels > > > i am basically trying to segregate the samples into 3 parts > containing > normal, HSIL and SCC data and this is the code that i have used > till now... > > setwd("E:\\Project\\CEL files\\Old\\GSE7803-3") > > f1=list.celfiles(path="E:\\__Project\\CEL > files\\Old\\GSE7803-3") > x1<-ReadAffy(filenames=f1) > pd<- data.frame(population = c(1,1,1,1,1,1,1,1,1,1,2, 2, > > + 2,2,2,2,2,3,3,3,3,3,3,3,3,3,3,__3,3,3,3,3,3,3,3,3,3,3), > + replicate= c(1,2,3,4,5,6,7,8,9,10,1,2,3,__4,5,6,7, > + 1,2,3,4,5,6,7,8,9,10,11,12,13,__14,15,16,17,18,19,20,21)) > > rownames(pd)<- sampleNames(x1) > v1<- list(population = "1 is normal, 2 is HSIL, 3 is SCC", > > replicate="arbitary numbering") > > > i further wish to perform rma and then generate a MA plot. > > kindly help me rectify this error and if possible explain with > an example > so that i could proceed further. > > [[alternative HTML version deleted]] > > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >