On 06/13/2011 06:23 AM, ascendo wrote:
Dear R-help
Hi,
I'm Won.
I try to do microarray normalization by R.
I use justRMA function within affy package, got error about segment fault.
I don't know why it happen.
I attached error below.
Hi Won -- as suggested, post to the Bioconductor mailing list
https://stat.ethz.ch/mailman/listinfo/bioconductor
Make sure that you've installed and updated your packages following the
Bioconductor protocol; problems can arise when package versions are not
matched correctly.
http://bioconductor.org/install/
You include the output of your script, but not the commands. Include the
commands, and include the output of sessionInfo(). If at all possible
make the example reproducible, e.g., by using the examples in the
package or data provided by the sample data sets. For instance after
source('http://bioconductor.org/biocLite.R')
biocLite(c("affy", "AffymetrixDataTestFiles"))
Run these commands
library(affy)
library(AffymetrixDataTestFiles)
sessionInfo()
cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A",
"2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles")
res <- just.rma(cel)
which produces
> library(affy)
> library(AffymetrixDataTestFiles)
> sessionInfo()
R version 2.12.2 Patched (2011-02-25 r54588)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_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] AffymetrixDataTestFiles_0.1.2 affy_1.28.0
[3] Biobase_2.10.0
loaded via a namespace (and not attached):
[1] affyio_1.18.0 preprocessCore_1.12.0
> cel <- system.file("rawData", "FusionSDK_HG-U133A", "HG-U133A",
+ "2.Calvin", "ethan1-1.CEL", package="AffymetrixDataTestFiles")
> res <- just.rma(cel)
Warning message:
In just.rma(cel) : Incompatible phenoData object. Created a new one.
Martin
Please help me.
Thank you.
Cheers,
Won
=======================
OS : Redhat linux
Cpu : intel xeon X5570
Memory : 26Gb
&
OS : Ubuntu
Cpu : intel q6600
Memory : 8Gb
=======================
Loading required package: Biobase
Loading required package: methods
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: gcrma
Loading required package: preprocessCore
Attaching package: 'affyPLM'
The following object(s) are masked from 'package:stats':
resid, residuals, weights
*** caught segfault ***
address 0xc609000, cause 'memory not mapped'
Traceback:
1: .Call("rma_c_complete", probeintensities$pm, pNList, ngenes,
normalize, background, bgversion, verbose, PACKAGE = "affy")
2: just.rma(filenames = l$filenames, phenoData = l$phenoData, description =
l$description, notes = notes, compress = compress, rm.mask = rm.mask,
rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose,
normalize = normalize, background = background, bgversion = bgversion,
destructive = destructive, cdfname = cdfname)
3: justRMA()
aborting ...
/var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation
fault /home01/e133ywc/R/R-2.13.0/bin/Rscript
/scratch/e133ywc/big/198/198.R
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