[BioC] arrayQualityMetrics: huge object size!?

[Shi, Tao]

Hi Audrey and list,

I'm just wondering why the object returned by "arrayQualityMetrics" function has such enormous size?  In fact, when I saved it out into a RData file, the resulting file is ~17GB big.  Is this normal or there was something wrong?


Thanks!

...Tao



> x <- ReadAffy(widget=TRUE)  ## x contains 111 affy133 plus2 chips of data
> xQC <- arrayQualityMetrics(expressionset = x, outdir = "QC", force = TRUE, do.logtransform = TRUE)
> object.size(x)
64040 bytes
> object.size(xQC)
407701944 bytes
> 
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-redhat-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=C                 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     

loaded via a namespace (and not attached):
 [1] affy_1.32.1                affyio_1.22.0             
 [3] affyPLM_1.30.0             annotate_1.32.1           
 [5] AnnotationDbi_1.16.11      arrayQualityMetrics_3.10.0
 [7] beadarray_2.4.1            Biobase_2.14.0            
 [9] BiocInstaller_1.2.1        Biostrings_2.22.0         
[11] Cairo_1.5-1                cluster_1.14.2            
[13] DBI_0.2-5                  genefilter_1.36.0         
[15] grid_2.14.1                Hmisc_3.9-2               
[17] hwriter_1.3                IRanges_1.12.5            
[19] lattice_0.20-0             latticeExtra_0.6-19       
[21] limma_3.10.2               preprocessCore_1.16.0     
[23] RColorBrewer_1.0-5         RSQLite_0.11.1            
[25] setRNG_2009.11-1           splines_2.14.1            
[27] survival_2.36-12           SVGAnnotation_0.9-0       
[29] tools_2.14.1               vsn_3.22.0                
[31] XML_3.9-4                  xtable_1.7-0              
[33] zlibbioc_1.0.0