On Fri, Jan 14, 2011 at 3:26 PM, Peevi Ijkl <ipeevi@yahoo.com> wrote:

> hello list
> I know i have been asking the same question over and over again but i just
> want
> to make sure am clear.
> I am loading the CEL files into R using ReadAffy along with the
> phenodata..then
> I am performing normalization.Now i want to create another expression set
> object
> which I can use for meta-analysis but I am not able to.Any suggestions will
> be
> helpful.
> thanks
> peevi
>
> 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)
> f1 <- function( x ) ( IQR(x) > 0.5 )
> ff <- filterfun(f1)
> rma_filtered <- genefilter( rma_expression_data, ff )
> sum(rma_filtered)
> rma_data_selected <- rma_expression_data [ rma_filtered, ]
> dim(rma_expression_data)
> dim(rma_data_selected)
>
> till here I have no errors at all..after this i try the following..
>
>
> data1<-new("ExpressionSet",exprs=rma_data_selected,phenodata=pData,annotation="hgu133a2")
>

Hi, Peevi.

"pData" in the above line is not a variable that you defined in the code
above.  If it was defined elsewhere, it is a bad choice of variable names
because there is a method called pData.  If it was not defined by you, that
is probably the problem and you want to use "pd" instead of "pData".

You still NEED to provide the output of sessionInfo() for EVERY email at
least once and NEED to provide the output of traceback() for every error
message.

Sean



>
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "annotatedDataFrameFrom",
> for
> signature "ExpressionSet".
>
> please help!
>
>
>
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>
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