[BioC] arrayQualityMetrics: huge object size!?

[Wolfgang Huber]

Dear Tao

this is possible, since the object contains all sorts of information 
that were computed during the report production, including graphics 
objects. The function was designed to allow for convenient 'picking out' 
of report information computationally, not for memory efficiency.

For more fine-grained control, please have a look at the vignette 
"Advanced topics: Customizing arrayQualityMetrics reports and 
programmatic processing of the output".

	Best wishes
	Wolfgang



Feb/27/12 6:46 PM, Shi, Tao scripsit::
> 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
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber