Dear All: Thank you all for your timely and valuable suggestions in trying to help out in installing the mapping10kxbar142 to R. Unfortunately, none worked though. The most promising method given by James attached below worked well until the last step that need to build an R-package. When in R I trye: >makePDpackage("Mapping10K_Xba142.cdf","Mapping10K_Xba142.csv", "Mapping10K_Xba142_probe_fasta", type = "SNP") R gave: >>>>>>>>>> Assuming Affymetrix Chip The package will be called pdmapping10kxba142 SNP Array Reading Mapping10K_Xba142.cdf Magic number is not 67. This is probably not a binary cdf file. >>>>>>>>>>> Any suggestions? Thanks, Jacob Zhang ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Original suggestions: ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ It is simple to do. First install R-2.2.0dev, run biocLite() to install necessary packages, then install.packages2("makePlatformDesign", getAllDeps = TRUE). Next, get these two files http://www.affymetrix.com/Auth/analysis/downloads/taf/Mapping10K_Xba14 2_ annot_csv.zip http://www.affymetrix.com/Auth/analysis/downloads/data/Mapping10K_Xba1 42 _probe_fasta.zip put these in the same directory (after unzipping) as your cdf file (this should be your working directory). Then type makePDpackage("Mapping10K_Xba142.cdf","Mapping10K_Xba142.csv", "Mapping10K_Xba142_probe_fasta", type = "SNP") This will make a package that you can install using R CMD INSTALL. If you are on Linux, you can install this directly. If you are on windows or MacOS you may need to get some tools. See the R-FAQ for these operating systems. As Rafa noted in an earlier response to your email, you would then need the oligo package to analyze these data. Since we are still actively working on this package, things are not well documented so it will take some work on your part to do any analyses. HTH, Jim This email message, including any attachments, is for the so...{{dropped}}

Zhang, Jacob (Zhongfa) wrote: > Dear All: > > Thank you all for your timely and valuable suggestions in trying to > help out in installing the mapping10kxbar142 to R. Unfortunately, none > worked though. The most promising method given by James attached below > worked well until the last step that need to build an R-package. When > in R I trye: > > >>makePDpackage("Mapping10K_Xba142.cdf","Mapping10K_Xba142.csv", > > "Mapping10K_Xba142_probe_fasta", type = "SNP") > > R gave: > > Assuming Affymetrix Chip > The package will be called pdmapping10kxba142 > SNP Array > Reading Mapping10K_Xba142.cdf > Magic number is not 67. This is probably not a binary cdf file. Ah, this is an incorrect assumption on my part. The cdffile is not binary, and a quick look indicates that Affy is still using their previous setup for the 10k chip, so it is incorrect to tell makePDpackage that the chip is a SNP chip (as odd as that may seem). When Affy switched from the 10k to 100k SNP chips, they made some fundamental changes in the chip design. The 10k chips are very similar in many ways to the expression arrays, so the existing functionality for the expression arrays will work with these chips as well. You can make a package for these chips in one of two ways: library(makecdfenv) make.cdf.package("Mapping10K_Xba142.cdf") and then install using R CMD INSTALL. You would then use the affy package to read in the celfiles and compute expression values for each SNP. Unfortunately, that is the extent of functionality in the affy package for these chips, so any other analyses will require you to write your own functions. Alternatively you can do: library(makePlatformDesign) makePDpackage("Mapping10K_Xba142.cdf", "Mapping10K_Xba142_probe_fasta") and install using R CMD INSTALL. You would then use the oligo package to read in the celfiles and possibly compute expression values. At this point you would have to look at the functions in oligo and see if they are applicable to your chip. Since the oligo package is designed to work with most oligonucleotide chips it should ultimately contain functionality to analyze your chips. However, it is still under development so the functions may or may not be in existence as yet. If you do use the oligo package, any feedback or bug reports you may have will be appreciated. It is probably not necessary to send them to the whole list. Instead, send to me, Rafael Irizarry, and Benilton Carvalho. You have my email address, and Rafa and Benilton's can be found by packageDescription("oligo"). Best, Jim > > > Any suggestions? > > Thanks, > > Jacob Zhang -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623