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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >-- >Best wishes >??? Wolfgang > >Wolfgang Huber >EMBL >http://www.embl.de/research/units/genome_biology/huber > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > >