[BioC] Using Affymetrix PM chips with Bioconductor

[Ben Bolstad]

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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