convert data in to expression set
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Nikul Soni ▴ 80
@nikul-soni-5917
Last seen 5.7 years ago
Sweden
I have my data in tab delimited file and i read it with read.delim function in R eset<-read.delim('expression_data.txt', header= T, row.names=1) i want to convert my eset object into Expressionset so that i can used it for plotting heatmaps after limma,s lmfit() finction according to the codes below. library("limma") f <- factor(as.character(eset$mol.biol)) design <- model.matrix(~f) fit <- eBayes(lmFit(eset,design)) selected <- p.adjust(fit$p.value[, 2]) <0.05 esetSel <- eset [selected, ] color.map <- function(mol.biol) { if (mol.biol=="ALL1/AF4") "#FF0000" else "#0000FF" } patientcolors <- unlist(lapply(esetSel$mol.bio, color.map)) heatmap(exprs(esetSel), col=topo.colors(100), ColSideColors=patientcolors) when i plot i have the error stated below heatmap(exprs(esetSel)) Error in function (classes, fdef, mtable) : unable to find an inherited method for function ‘exprs’ for signature ‘"data.frame"’ Please help me with the code. Nikul [[alternative HTML version deleted]]
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Jeremy Ng ▴ 180
@jeremy-ng-5464
Last seen 6.4 years ago
Singapore
Hi Nikul, You can do this with biobase. If your intensity is stored in a data frame called "data". To convert this to a ExpressionSet, use the following require(Biobase) object<-new("ExpressionSet", exprs=as.matrix(data)) "object" will be an expression set object containing just the intensity. Jeremy On Thu, Jun 20, 2013 at 3:50 PM, Nikul Soni <soninikul007@gmail.com> wrote: > I have my data in tab delimited file and i read it with read.delim function > in R > > eset<-read.delim('expression_data.txt', header= T, row.names=1) > > i want to convert my eset object into Expressionset so that i can used it > for plotting heatmaps after limma,s lmfit() finction according to the codes > below. > > library("limma") > f <- factor(as.character(eset$mol.biol)) > design <- model.matrix(~f) > fit <- eBayes(lmFit(eset,design)) > selected <- p.adjust(fit$p.value[, 2]) <0.05 > esetSel <- eset [selected, ] > color.map <- function(mol.biol) { if (mol.biol=="ALL1/AF4") "#FF0000" else > "#0000FF" } > patientcolors <- unlist(lapply(esetSel$mol.bio, color.map)) > heatmap(exprs(esetSel), col=topo.colors(100), ColSideColors=patientcolors) > > when i plot i have the error stated below > > heatmap(exprs(esetSel)) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function ‘exprs’ for signature > ‘"data.frame"’ > > Please help me with the code. > > Nikul > > [[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 > [[alternative HTML version deleted]]
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