[BioC] meta-analysis

[Steve Lianoglou]

Hi,

On Thu, Jan 13, 2011 at 6:36 PM, Peevi Ijkl <ipeevi at yahoo.com> wrote:
> Hilist
> i need some help regarding meta-analysis.I did the following..
>
> pd <- read.AnnotatedDataFrame( ".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)
> f1 <- function( x ) ( IQR(x) > 0.5 )
> ff <- filterfun(f1)
> rma_filtered <- genefilter( rma_data, ff )
> sum(rma_filtered)
> rma_data_selected <- rma_data [ rma_filtered, ]
> dim(rma_data)
> dim(rma_data_selected)
>
> cl <- as.numeric(pd$Condition == "" )
> cl
> ##multtest
> resT <- mt.maxT(rma_data_selected, classlabel=cl, B=2000 )
>
> ##Look at the first 10 probesets
> resT [1:10 , ]
> probe_sets <- rownames(resT) [1:100]
>
> ##Select the 1st 100 probsets
> resT7561<-resT[1:100,]
> resT7561
>
> I tried doing venn mapping on this data

How?

> ,but am getting the following error
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "exprs", for signature
> "data.frame"

I think the key point here is to figure out where this error is occurring.

Go back to the 20 or so lines of codes that you pasted, and look at
the 6th line:

rma_data <- exprs(rma_expression_data)

I guess this error must be happening there, right?

If so, then your error is on or before that line. Furthermore, there
should be even more errors that follow that one, no?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact