Hi Hyeong-Min, Essentially, making a cdf environment (which I have done) won't 100% work with the new ST generation of chips, because now, each probe can be a part of multiple probesets, whereas in the past, this was never the case. see https://stat.ethz.ch/pipermail/bioconductor/2007-June/017740.html If you are using OSX or a unix/linux system, then you may also want to look at apt-probeset-summarize from the Affymetrix Power Tools. I find it to be VERY fast (less than 2 mins for any reasonable size ~20 chip experiment). The equivalent on windows is the Affymetrix Expression Console. You will need the library file that Jim mentioned (from Affymetrix), and then it's a simple case of apt-probeset-summarize -a rma -p *pgf -c *clf -o ./normalised *CEL cheers, Mark On 15/07/2008, at 5:18 AM, Henrik Bengtsson wrote: > Hi, > > you can also take a look at the aroma.affymetrix. It handles common > preprocessing methods for basically all chip types with a CDF file. > All you need is a CDF file and the CEL files. Here I mean a *real* > CDF file and not a compiled Bioconductor "CDF" package. To install > aroma.affymetrix, go to > > http://groups.google.com/group/aroma-affymetrix > > Works with any OS and approx 1GB of RAM. Note also the comment on > http://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1 > that suggest that you convert the ASCII MoGene-1_0-st-v1.CDF from > Affymetrix into a binary CDF - that's easy with convertCdf() in > 'affxparser'. > > Cheers > > Henrik > > On Mon, Jul 14, 2008 at 11:33 AM, James W. MacDonald > <jmacdon at="" med.umich.edu=""> wrote: >> Hi Hyeong-Min, >> >> Lee, Hyeong-min wrote: >>> >>> Hello. >>> I'm looking for "mogene10stv1cdf" I couldn't find it on the >>> metadata.html. >>> Could you please tell me where I can get it? Thank you for your >>> time. >> >> Unfortunately, we don't as yet supply the cdf file for this chip >> type. >> >> There are a couple of ways you can analyze these data, but none >> involves the >> canonical makecdfenv/affy pipeline. >> >> You can use the successor to makecdfenv/affy, which is the >> pdInfoBuilder/oligo pipeline (more to follow on this), or the xps >> package. >> Non-BioC software includes aroma.affymetrix and Expression Console >> (Affymetrix's own software). >> >> To use oligo to do the analysis you will first need to create a >> pdInfo >> package. This package replaces all of the cdf, probe and annotation >> packages >> that you may be used to. In order to build this package you will >> need to >> download the library files (the first one on this page: >> http://www.affymetrix.com/support/technical/byproduct.affx?product =mogene-1_0-st-v1) >> , >> the probe file in tabular format, and the transcript cluster >> annotation csv >> file (both of which are found at the above URL). >> >> You then have to create a 'AffyGenePDInfoPkgSeed' object which you >> can then >> use to build the package. The help page for this doesn't really >> cover this >> sort of thing, so here is an example of how you would do so: >> >> pgfFile <- "MoGene-1_0-st-v1.r3.pgf" >> clfFile <- "MoGene-1_0-st-v1.r3.clf" >> transFile <- "MoGene-1_0-st-v1.na24.mm8.transcript.csv" >> probeFile <- "MoGene-1_0-st-v1.probe.tab" >> >> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email = >> "e at mail.net", version = "0.0.1", genomebuild = "thegenomebuilddate", >> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, >> transFile = transFile, probeFile = probeFile) >> >> makePdInfoPackage(pkg) >> >> At this point you need to install the package. In any case, this is >> done at >> a terminal prompt (or DOS prompt on Windows) using >> >> R CMD INSTALL thepackage >> >> You may also need to point to your library directory as well, using >> something like >> >> R CMD INSTALL -l /path/to/lib thepackage >> >> If you are on linux, this Will Just Work (tm). However, if you are on >> Windows or MacOS, you will need to get set up to build packages. >> Luckily >> this isn't nearly as involved as in the past. See the R >> Installation and >> Administration manual >> >> http://cran.r-project.org/doc/manuals/R-admin.html >> >> for your particular OS. >> >> Best, >> >> Jim >> >> >> >>> Best >>> Hyeong-Min Lee >>> Ph.D. candidate >>> Program in Neurobiology >>> Dept. Biomedical Sciences >>> College of Medicine, FSU >>> Lab; 850-645-2922 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor