[BioC] arrayQualityMetrics: huge object size!?
Wolfgang Huber
whuber at embl.de
Tue Feb 28 10:29:35 CET 2012
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
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