[BioC] Anyone Know how to make a fake CEL file?

[Rafael A. Irizarry]

to avoid the creation of "Cel files" that arent really Cel files
the function "write.celfile" will not be in affy 1.3. but i dont think 
you want to be making them anyways. i think what you want is to create fake 
instances of AffyBatches. As Laurent points out you want to leanr about 
cdfenvs. below is a quick example simulating probe level data for two 
arrays:

library(affy)
 
## fake environment
##it the below change the environment def must change too
NCOL <- 8
NROW <- 8
n <- NCOL*NROW
 
tmp <- sample(1:50)
dummy <- new.env(hash=T)
index <- cbind(tmp[1:10], tmp[11:20])
assign("gene.a", index, envir=dummy)
index <- cbind(tmp[21:30],tmp[31:40])
assign("gene.b", index, envir=dummy)
cat("done.\n")
 
samplenames <- c("sample1","sample2")
signal <- exp(rexp(n,1))
e <- cbind(exp(rnorm(n,4,1))+signal,exp(rnorm(n,4,1))+signal)
colnames(e) <- samplenames
pd <- read.phenoData(sampleNames=samplenames)
afbatch <- new("AffyBatch",
               exprs=e,
               phenoData=pd,
               cdfName="dummy",
               ncol=NCOL,nrow=NROW)
cat("done.\n")
 






On Tue, 14 Oct 2003, Laurent Gautier wrote:

> On Tue, Oct 14, 2003 at 02:22:34PM -0400, Park, Richard wrote:
> > I am trying to make a couple of fake cel files to represent a time course treatment between three time points. 
> > I am trying to test the effects of normalization on various possible treatments. 
> > Is there a way to make a fake CEL file? 
> 
> write.celfile
> (although sketchy for the headers customization and without 
> guaranty you can read it anywhere outside the package ;) ).
> 
> > and if there is, how do you know the corresponding x and y locations on the chip that correspond with the various affy ids? I know that this information is located in the various cdf files, but I am unaware of how to access that information. 
> > 
> 
> cdfenvs hold the key (doc scattered across different places, among which 
> the code unfortunately)
> 
> 
> > Thanks for any help, 
> > 
> > 
> > Richard Park 
> > Immunology - Computational Data Analyzer
> > Joslin Diabetes Center
> > Ph: 617-732-2482
> > Richard.Park at joslin.harvard.edu
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 

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| Rafael Irizarry			phone:	(410) 614-5157		|
| Assistant Professor			fax:	(410) 955-0958		|
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