I have affyio 1.10.1 -- which is the current release version ( http://bioconductor.org/packages/2.3/bioc/html/affyio.html). You seem to have a newer one. Ben Bolstad <bmb@bmbolstad.com> wrote on 03/23/2009 10:12:33 AM: > Ben Bolstad <bmb@bmbolstad.com> > 23-Mar-2009 10:12 AM > Message Size: 8.2 KB > > To > > James Mcininch <james.mcininch@biogenidec.com> > > cc > > bioconductor@stat.math.ethz.ch > > Subject > > Re: [BioC] Using Affymetrix PM chips with Bioconductor > > What version of affyio do you have installed? I have no problems > creating a cdfenv using this CDF. > > Ben > > > library(makecdfenv) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affy > Loading required package: affyio > > make.cdf.package("HT_HG-U133_Plus_PM.CDF", version="0.0.2", > + species="Homo_sapiens", maintainer="James McIninch > + <james.mcininch*at*biogenidec.com>") > Creating package in /tmp/hthgu133pluspmcdf > > > > README PLEASE: > A source package has now been produced in > /tmp/hthgu133pluspmcdf. > Before using this package it must be installed via 'R CMD INSTALL' > at a terminal prompt (or DOS command shell). > If you are using Windows, you will need to get set up to install > packages. > See the 'R Installation and Administration' manual, specifically > Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset' > for more information. > > Alternatively, you could use make.cdf.env(), which will not require you > to install a package. > However, this environment will only persist for the current R session > unless you save() it. > > > > sessionInfo() > R version 2.8.1 (2008-12-22) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.u tf8;LC_MONETARY=C;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C ;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATI ON=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] makecdfenv_1.21.0 affyio_1.11.1 affy_1.20.0 > Biobase_2.2.0 > > loaded via a namespace (and not attached): > [1] preprocessCore_1.5.1 > > > > > > > On Mon, 2009-03-23 at 09:42 -0400, James Mcininch wrote: > > I'm looking on some advice with regard to setting up to use the newer > > Affymetrix PM chips with BioConductor... Specifically HT HG-U133A+ PM, HT > > MG-430 PM, and HT Rat-230 PM plates. > > > > Way back when, you would make cdf and probe packages using > > make.cdf.package() and makeProbePackage() from the makecdfenv and > > matchprobesets libraries. However, this doesn't seem to work for the PM > > chip CDFs downloaded from Affymetrix. > > > > make.cdf.package crashes R when applied to HG-U133A, it works for MG-430, > > and runs for Rat-230 but never completes (just locks a CPU at 100% all > > day). When I try to makeProbePackage on the mouse chip, it runs for ~10 > > sec and fails with the error: "Error in rep(NA, max(pm1, mm1, pm2, mm2)) : > > invalid 'times' argument" -- this is using BioConductor 2.3 and R 2.8.1. I > > haven't gotten as far as trying to make annotation packages, but I seem to > > recall that I need a probe package first... > > > > Presumably, someone out there has already broached these issues. Also, it > > seems to me that the PM chips throw a little wrench into the whole thing > > because there's no mismatch probes - perhaps the CDF format is changed and > > this is the problem (I can't tell, it's binary)? Any guidance on how to > > make these packages? > > > > Perhaps I am wasting my time... Should I be looking to learn > > aroma.affymetrix? I have a number of people that have processes designed > > around the non-HT/non-PM chips that would really like to modify their > > workflows as little as possible, but I'm not sure if that's practical. > > > > For what it's worth, I get something like this when doing make.cdf.package > > on the human CDF: > > > > > make.cdf.package("HT_HG-U133_Plus_PM.CDF", version="0.0.2", > > species="Homo_sapiens", maintainer="James McIninch > > <james.mcininch*at*biogenidec.com>") > > *** glibc detected *** /usr/lib64/R/bin/exec/R: malloc(): memory > > corruption: 0x000000001ef51cc0 *** > > ======= Backtrace: ========= > > /lib64/libc.so.6[0x32cfe724ac] > > /lib64/libc.so.6(__libc_malloc+0x7a)[0x32cfe7402a] > > /usr/lib64/R/lib/libR.so(Rf_allocVector+0x881)[0x2b829891eef1] > > /usr/lib64/R/lib/libR.so(Rf_allocMatrix+0x6a)[0x2b829882739a] > > /usr/lib64/R/library/affyio/libs/affyio.so(ReadCDFFile+0x1cb) > [0x2b829db9e75b] > > /usr/lib64/R/lib/libR.so[0x2b82988bc0cd] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x698)[0x2b82988ee3c8] > > /usr/lib64/R/lib/libR.so[0x2b82988f26b3] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so[0x2b82988eeef2] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so[0x2b82988eeef2] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so(Rf_applyClosure+0x299)[0x2b82988f0589] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x311)[0x2b82988ee041] > > /usr/lib64/R/lib/libR.so[0x2b82988f26b3] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so[0x2b82988eeef2] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x46b)[0x2b82988ee19b] > > /usr/lib64/R/lib/libR.so(Rf_applyClosure+0x299)[0x2b82988f0589] > > /usr/lib64/R/lib/libR.so(Rf_eval+0x311)[0x2b82988ee041] > > /usr/lib64/R/lib/libR.so(Rf_ReplIteration+0x188)[0x2b82989164a8] > > /usr/lib64/R/lib/libR.so[0x2b82989167ac] > > /usr/lib64/R/lib/libR.so(run_Rmainloop+0x50)[0x2b8298916b60] > > /usr/lib64/R/bin/exec/R(main+0x1b)[0x40080b] > > /lib64/libc.so.6(__libc_start_main+0xf4)[0x32cfe1d974] > > /usr/lib64/R/bin/exec/R[0x400709] > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]