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@joslin.harvard.edu > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- +--------------------------------------------------------------------- --+ | Rafael Irizarry phone: (410) 614-5157 | | Assistant Professor fax: (410) 955-0958 | | Department of Biostatistics office: E3035 | | Johns Hopkins University email: rafa@jhu.edu | +--------------------------------------------------------------------- --+