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

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> pd <- read.AnnotatedDataFrame("target.txt",header=TRUE,row.names=1,as.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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