[BioC] arrayQualityMetrics: huge object size!?

[Shi, Tao]

Thank you, Wolfgang!  I'll take look at that.

...Tao




>________________________________
> From: Wolfgang Huber <whuber at embl.de>
>To: bioconductor at r-project.org 
>Sent: Tuesday, February 28, 2012 1:29 AM
>Subject: Re: [BioC] arrayQualityMetrics: huge object size!?
> 
>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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