Question: Anyone Know how to make a fake CEL file?
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gravatar for Park, Richard
15.9 years ago by
Park, Richard220
Park, Richard220 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? 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. Thanks for any help, Richard Park Immunology - Computational Data Analyzer Joslin Diabetes Center Ph: 617-732-2482 Richard.Park@joslin.harvard.edu
normalization cdf affy • 401 views
ADD COMMENTlink modified 15.9 years ago by Laurent Gautier2.2k • written 15.9 years ago by Park, Richard220
Answer: Anyone Know how to make a fake CEL file?
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gravatar for Laurent Gautier
15.9 years ago by
Laurent Gautier2.2k
Laurent Gautier2.2k 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 -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
ADD COMMENTlink written 15.9 years ago by Laurent Gautier2.2k
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 | +--------------------------------------------------------------------- --+
ADD REPLYlink written 15.9 years ago by Rafael A. Irizarry2.3k
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