Hi all, I'm trying to use affy package to normalize (RMA normalization) the intensity values in some ".cel" files for the species /Rhodobacter //sphaeroides. /However, I can not find the corresponding "CDF" file from bioconductor web site. (i.e. the MetaData section does not contain that species's CDF package.) Does anyone know where to get the CDF file for /Rhodobacter /or any idea how to "RMA" normalize the .cel files for it? thanks, Yue / /

Yue Pan wrote: > Hi all, > > I'm trying to use affy package to normalize (RMA normalization) the > intensity values in some ".cel" files for the species /Rhodobacter > //sphaeroides. /However, I can not find the corresponding "CDF" file > from bioconductor web site. (i.e. the MetaData section does not contain > that species's CDF package.) AFAIK, this isn't a commercially available Affy chip, so we don't have access to the CDF file. I would think that whomever you got the chip or chip data from would have the CDF, as this is part of the deal with a custom chip. I would suggest contacting them. Once you have the CDF, you will need to make a cdfenv using the makecdfenv package. See ?make.cdf.env for more details. If you wish to make an installed package, see ?make.cdf.package. Note that if you are on windows, you will need to get set up to install source packages before you will be able to use the results of this function. For this, see the R-FAQ for Windows #3.1. For further information about installing packages see 'Writing R Extensions' and 'R Installation and Administration'. HTH, Jim > > Does anyone know where to get the CDF file for /Rhodobacter /or any idea > how to "RMA" normalize the .cel files for it? > > thanks, > Yue > / > > / > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.