This problem may well be due to the repeated R_alloc calls, and might be
fixable by refactoring the code, but I am not sure that is the answer here.
This package is designed for the 3' biased arrays (and works well enough for
them), and isn't intended to be used for the newer random primer arrays. The
makecdfenv/affy packages have been supplanted by the pdInfoBuilder/oligo
packages for the newer generation of arrays.
Crispin Miller's group was able to get makecdfenv to work by stripping out the
background probes first, and have cdf packages available on their website if
the end user insists on using affy for this array:
http://xmap.picr.man.ac.uk/download
which by the way appears to be down now.
Anyway, the supported methods of analyzing these chip types are listed in the
workflows page
http://www.bioconductor.org/docs/workflows/oligoarrays/
and you will note that makecdfenv/affy is not one of them.
Best,
Jim
Martin Morgan mtmor...@fhcrc.org 12/28/09 2:09 PM
Peng Yu wrote:
My machine has 8GB memory. I had quit all other programs that might
take a lot of memory when I try the script (before I post the first
message in this thread). The cdf file is of only 741 MB. It is strange
to me to see the error.
For me this tops out at about 13 gigs.
The reason is I think in the C-level implementation details. R_alloc is
called repeatedly during file parsing, where likely the author intends
to Calloc / Free.
Martin
On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber whu...@embl.de wrote:
Dear Peng Yu
how big is the RAM of your computer? You could try with closing all other
applications before running this script. You could try on a server with more
RAM.
I tried downloading the file whose URL who give below, but gave up after
some failed rounds with the extraordinarily annoying and intrusive
registration procedure that Affymetrix has set up for this. Let us know how
it goes with the suggestions above, if they don't help, I'd try again with
that.
Best wishes
Wolfgang
I run the following example. The cdf file is downloaded from the
following link. I'm wondering what the problem is with
make.cdf.package.
http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx-1_0-st-v1.text.cdf.zip
$ Rscript MoEx-1_0-st-v1.cdf.R
library(makecdfenv)
Loading required package: Biobase
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
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1
loaded via a namespace (and not attached):
[1] preprocessCore_1.8.0
make.cdf.package('MoEx-1_0-st-v1.text.cdf', species='Mus_musculus')
Reading CDF file.
Error: cannot allocate vector of size 1 Kb
Execution halted
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