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]
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