Hi list..
I am trying to create an expression set object..here is what i did so far..

pd <- read.AnnotatedDataFrame( "target.txt", header=T, row.names=1, sep=";" )
pData(pd)
expression_data <- ReadAffy( filenames = rownames (pData(pd)) ) 
expression_data
rma_expression_data <-rma(expression_data)
rma_data <- exprs(rma_expression_data)

now i want to create an expression set object from the above using the 
following:
ALLSet <- new("ExpressionSet", exprs =rma_data, phenoData = pd,
+ annotation = "hgu95av2")
but I am getting the following error when i use the above

Error in validObject(.Object) : 
  invalid class "ExpressionSet" object: 1: row numbers differ for assayData 
members
invalid class "ExpressionSet" object: 2: sample numbers differ for assayData 
members

while if i use rma_expression_data at the highlighted area am getting the 
following error:
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "annotatedDataFrameFrom", for 
signature "ExpressionSet"

any help would be appreciated.

thanks
peevi



      
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