Hi, yesterday I've started to make a cdf environment for the U133_X3P chip. Unfortunately, I had to stop the process after several hours for some reasons. Before I will start to run make.cdf.env() again, I would like to ask you if anyone of you has made such an U133_X3P environment. Another question I have is how long it approximately takes to make such an environment (on, e.g., a computer with 2GHz and 512 MB RAM). I was told that this chip is comparable with the Human Genome U133 Plus 2.0 Array. Thanks a lot, Holger -- Ab sofort DSL-Tarif ohne Grundgebühr: http://www.gmx.net/dsl

Hi Holger, I just made the cdf environment for this chip, and it should be posted on the BioC website within the next few days. It only took maybe five minutes to run make.cdf.env(), and then maybe two minutes to compile the binary. However, this cdf is huge (seems to be much larger than the U133_Plus_2), so I doubt that 512 Mb RAM is going to be enough. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Holger Schwender" <holger.schw@gmx.de> 04/21/04 09:03AM >>> Hi, yesterday I've started to make a cdf environment for the U133_X3P chip. Unfortunately, I had to stop the process after several hours for some reasons. Before I will start to run make.cdf.env() again, I would like to ask you if anyone of you has made such an U133_X3P environment. Another question I have is how long it approximately takes to make such an environment (on, e.g., a computer with 2GHz and 512 MB RAM). I was told that this chip is comparable with the Human Genome U133 Plus 2.0 Array. Thanks a lot, Holger -- Ab sofort DSL-Tarif ohne Grundgeb?hr: http://www.gmx.net/dsl _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Hi Holger it should not take that much time to create a CDF environment / package. Did you observe that your machine started to do a lot of swapping? Have a look at the function make.cdf.env in the file make.cdf.env.R in the R subdirectory of the package. I suggest that you run library(makecdfenv) debug(make.cdf.env) make.cdf.package(.... ) and step through the process - and report at which point the package "hangs"! Best wishes Wolfgang Holger Schwender wrote: > Hi, > > yesterday I've started to make a cdf environment for the U133_X3P chip. > Unfortunately, I had to stop the process after several hours for some > reasons. Before I will start to run make.cdf.env() again, I would like to > ask you if anyone of you has made such an U133_X3P environment. Another > question I have is how long it approximately takes to make such an > environment (on, e.g., a computer with 2GHz and 512 MB RAM). I was told that > this chip is comparable with the Human Genome U133 Plus 2.0 Array. > > Thanks a lot, > Holger > -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber