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.
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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