arrayQualityMetrics: huge object size!?
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Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
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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@wolfgang-huber-3550
Last seen 4 days ago
EMBL European Molecular Biology Laborat…
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
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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 > > >
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