Using Affymetrix PM chips with Bioconductor
1
0
Entering edit mode
@james-mcininch-3356
Last seen 9.5 years ago
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)[0x2b829d b9e75b] /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]]
Annotation cdf probe makecdfenv Annotation cdf probe makecdfenv • 1.2k views
ADD COMMENT
0
Entering edit mode
Ben Bolstad ★ 1.2k
@ben-bolstad-1494
Last seen 6.6 years ago
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)[0x2b82 9db9e75b] > /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 at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENT
0
Entering edit mode
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]]
ADD REPLY

Login before adding your answer.

Traffic: 769 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6