I am interested to know how can i access vector of a column in phenotype data frame if  i don't know the conditions(groups) name in the phenotype data frame . I have phenotype information in the below file

Files                    Groups
GSM248652.CEL   A
GSM248655.CEL   A
GSM248238.CEL   A
GSM248650.CEL   B
GSM248651.CEL   B
GSM248661.CEL   C
GSM248660.CEL   C

Here in the above file i have Groups column and i normally access it and design a model matrix by

pdata = read.AnnotatedDataFrame("file.txt",sep="")
unique <- unique(pdata$Groups)
f <- factor(pdata$Groups, levels=unique)  
  design <- model.matrix(~0+f)
  colnames(design) <- unique 

Now i don't know the column name of conditions(groups), how to access and design a model matrix. Help appreciated.

According to the information pasted above, i think this should work.

You can read the file by read.table(), and then access the respective column vector to design a model matrix.

  pdata <- read.table("file.txt",header=TRUE)
  unique <- unique(pdata[,2])
  f <- factor(pdata[,2],levels=unique)
  design <- model.matrix(~0+f)
  colnames(design) <- unique