I 'm going to explain how I create my exprSet object (I'm working with 3 
replicates)

If you don't understand something , please ask me


>  library(Biobase)
>  COLlabels<-c("Array","Type")
>  COLlabels
        [1] "Array" "Type"

>
        ROWlabels<-c("rep1_Exp","rep1_Co","rep2_Exp","rep2_Co","rep3_Exp","rep3_Co")

>  ROWlabels
        [1] "rep1_Exp" "rep1_Co" "rep2_Exp" "rep2_Co" "rep3_Exp"
        [6] "rep3_Co"

>  phD <- read.delim("path/phenoDataFile.txt", header=FALSE,
        row.names=ROWlabels, col.names=COLlabels)

            /phenoDataFile.txt is a text-tabulated file like this one:
            /

            /1       Experiment
            1       Control
            2       Experiment
            2       Control
            3       Experiment
            3       Control
            /

>  phD
                  Array       Type
        rep1_Exp    1      Experiment
        rep1_Co     1      Control
        rep2_Exp    2      Experiment
        rep2_Co     2      Control
        rep3_Exp    3      Experiment
        rep3_Co     3      Control

>  CLabels<-list("Array","Type")

>  CLabels
        [[1]]
        [1] "Array"
         
        [[2]]
        [1] "Type"

>  pD<-new("phenoData",pData=phD, varLabels=CLabels)

>  pD
                 phenoData object with 2 variables and 6 cases
                 varLabels
                        : Array
                        : Type


>  table <- read.delim("path/affyLOG.txt",header=TRUE,row.name=1)

            /affyLog.txt is a text-tabulated file. Rows are the probes
            (or genes) and columns the chips:
            /           rep1_Exp   rep1_Co   rep2_Exp   rep2_Co  
            rep3_Exp    rep3_Co 
            gene 1         x        x           x         x         x  
                    x
            gene 2         x        x           x         x         x  
                    x
            gene 3         x        x           x         x         x  
                    x
            gene 4         x        x           x         x         x  
                    x
            gene 5         x        x           x         x         x  
                    x
            ....
            /
            x are the intensity values
            /


>  matriz <- as.matrix(table)
>  eSet <- new("exprSet", exprs=matriz, phenoData=pD)
>  eSet
        Expression Set (exprSet) with
                22283 genes
                6 samples
                         phenoData object with 2 variables and 6 cases
                 varLabels
                        : Array
                        : Type






Khan, Sohail wrote:

>Dear List,
> 
>I am trying to create an exprSet object from a tab delimited file where first column contains the gene names and remaining 14 columns contain the expression data.  I am using the function read.exprSet() to read the file.  However, when I look at pData(), I see that the gene name columns is listed as the sample.  How can creat an exprSet object correctly?  Thanks in advance.
> 
>-Sohail
>
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