Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type "Cellline/xenograft",tumor="primary,secondary,cellline",time "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9") # Initialize exprSet object pD <- new("phenoData", pData=pd, varLabels=pdN); # This is my eSet!!! metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), phenoData=pD) I get the following error: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Can someone suggest me how to use the new method AnnotatedDataFrame to create eSet? Thanks Manisha [[alternative HTML version deleted]]
Hi Manisha -- this is a bioconductor package, so ask on the Bioconductor mailing list. The 'exprSet' class is quite old, and has been replaced by the 'ExpressionSet' class. Update your venison of R and Bioconductor (http://bioconductor.org/download). Then evaluate the commands> library(Biobase) > openVignette()and read the first vignette 'Biobase - An introduction to Biobase and ExpressionSets'. Hope that helps, Martin "Manisha Brahmachary" <mb3058 at c2b2.columbia.edu> writes:> Hi, > > > > I am having troubles with creating an eSet and would appreciate any help on > the following problem. > > > > I am trying to create an eSet using the following code > > > > pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); > > colnames(pd) <- c("type","tumor","time","id"); > > pdN <- list(type > "Cellline/xenograft",tumor="primary,secondary,cellline",time > "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9") > > # Initialize exprSet object > > pD <- new("phenoData", pData=pd, varLabels=pdN); > > # This is my eSet!!! > > metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), > phenoData=pD) > > > > I get the following error: > > > > The phenoData class is deprecated, use AnnotatedDataFrame (with > ExpressionSet) instead > > > > > > Can someone suggest me how to use the new method AnnotatedDataFrame to create > eSet? > > > > > > Thanks > > > > Manisha > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
Hi Manisha, This is a Bioconductor-specific question. Please repost on the bioc listserv: bioconductor at stat.math.ethz.ch Best, Jim Manisha Brahmachary wrote:> Hi, > > > > I am having troubles with creating an eSet and would appreciate any help on > the following problem. > > > > I am trying to create an eSet using the following code > > > > pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); > > colnames(pd) <- c("type","tumor","time","id"); > > pdN <- list(type > "Cellline/xenograft",tumor="primary,secondary,cellline",time > "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9") > > # Initialize exprSet object > > pD <- new("phenoData", pData=pd, varLabels=pdN); > > # This is my eSet!!! > > metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), > phenoData=pD) > > > > I get the following error: > > > > The phenoData class is deprecated, use AnnotatedDataFrame (with > ExpressionSet) instead > > > > > > Can someone suggest me how to use the new method AnnotatedDataFrame to create > eSet? > > > > > > Thanks > > > > Manisha > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
Reasonably Related Threads
- Error in function (classes, fdef, mtable): unable to find an inherited method for function "indexProbes", for signature "exprSet", "character"
- FW: Selecting undefined column of a data frame (was [BioC] read.phenoData vs read.AnnotatedDataFrame)
- Can't make affylmGUI work
- S4 Method Collisions with "[" (PR#4075)
- A problem subsetting a data frame