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
>
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