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.utf8;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_IDENTIFICATION=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]]
> > 
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