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Manuela Di Russo
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70
@manuela-di-russo-4778
Last seen 10.2 years ago
Dear all,
I have some problems with the error "cannot allocate vector of
size..."
I am using the Bioc package "arrayQualityMetrics" to assess the
quality of a microarray experiment saved in an Affybatch object
(rawData) but I encountered the same problem with oneChannelGUI
package, when I apply the gcrma function.
My pc has 3.37 GB RAM.
I read several posts in the mailing list and I changed some parameters
to increase the memory limit. For example I used the command
memory.limit (4095), I set paging file dimensions to 4092 MB (it was
2046 MB) and I used the 3 GB switch in the Boot.ini file in order to
increase the virtual address space of processes and applications.
Moreover I reduced the code lines in a single session to the strictly
necessary commands.
R version 2.14.1 (2011-12-22)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)
> memory.limit(4095)
[1] 4095
> setwd("C:/BACKUP/Dati/Progetti/Landi/meta-analisi MPM/GSE12345_RAW")
> library(affy)
Carico il pacchetto richiesto: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
> pd <- read.AnnotatedDataFrame("target.txt",header=TRUE,row.names=1,a
s.is=TRUE)
> rawData <- read.affybatch(filenames=pData(pd)$FileName,phenoData=pd)
> library(arrayQualityMetrics)
> a<-arrayQualityMetrics(rawData, outdir = "RawData QualityMetrics
Report",force = TRUE, do.logtransform = TRUE)
The report will be written into directory 'RawData QualityMetrics
Report'.
Loading required package: AnnotationDbi
Errore: cannot allocate vector of size 30.0 Mb
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu133plus2cdf_2.9.1 AnnotationDbi_1.16.17
[3] arrayQualityMetrics_3.10.0 affy_1.32.1
[5] Biobase_2.14.0
loaded via a namespace (and not attached):
[1] affyio_1.22.0 affyPLM_1.30.0 annotate_1.32.1
[4] beadarray_2.4.1 BiocInstaller_1.2.1 Biostrings_2.22.0
[7] Cairo_1.5-1 cluster_1.14.2 DBI_0.2-5
[10] genefilter_1.36.0 grid_2.14.1 Hmisc_3.9-2
[13] hwriter_1.3 IRanges_1.12.6 lattice_0.20-0
[16] latticeExtra_0.6-19 limma_3.10.2 preprocessCore_1.16.0
[19] RColorBrewer_1.0-5 RSQLite_0.11.1 setRNG_2009.11-1
[22] splines_2.14.1 survival_2.36-12 SVGAnnotation_0.9-0
[25] tools_2.14.1 vsn_3.22.0 XML_3.9-4.1
[28] xtable_1.7-0 zlibbioc_1.0.0
> traceback()
4: density.default(as.matrix(log2(x$pm)))
3: density(as.matrix(log2(x$pm)))
2: aqm.pmmm(x)
1: arrayQualityMetrics(rawData, outdir = "RawData QualityMetrics
Report",
force = TRUE, do.logtransform = TRUE)
Can anyone suggest anything?
Thank you!
Have a nice day!
Manuela
----------------------------------------------------------------------
------------------
Manuela Di Russo, Ph.D. Student
Department of Experimental Pathology, MBIE
University of Pisa
Pisa, Italy
e-mail: manuela.dirusso@for.unipi.it
tel: +39050993538
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