arrayQualityMetrics
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Al Ivens ▴ 270
@al-ivens-1646
Last seen 9.6 years ago
Hi, I have been using arrayQualityMetrics, and find it very useful. However, to make it even more useful, would it be possible to have legends for some of the plots, e.g. density/ecdf, RNAdeg incorporated in the output? Cheers and thanks, a > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 simpleaffy_2.14.05 [5] affyPLM_1.14.0 gcrma_2.10.0 matchprobes_1.10.0 RColorBrewer_1.0-2 [9] vsn_3.2.1 limma_2.12.0 affy_1.16.0 preprocessCore_1.0.0 [13] affyio_1.6.1 genefilter_1.16.0 survival_2.34 geneplotter_1.16.0 [17] lattice_0.17-2 annotate_1.16.1 xtable_1.5-2 AnnotationDbi_1.0.6 [21] RSQLite_0.6-4 DBI_0.2-4 Biobase_1.16.1 loaded via a namespace (and not attached): [1] KernSmooth_2.22-21 > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
cdf arrayQualityMetrics cdf arrayQualityMetrics • 1.2k views
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audrey ▴ 280
@audrey-2551
Last seen 9.6 years ago
Hi Al, Thank you for the useful feedback. In the development version of arrayQualityMetrics, I have added a legend with the name of the experiments on the density and ecdf plots. I will think about adding the same on the RNAdeg plot in the next version. However when there are too many experiments there is not enough place on the plot to write all the experiment names so I advice you in that case to use the argument "split.plots" of arrayQualityMetrics and to set it at 20 maximum. Thank you, Audrey Al Ivens wrote: > Hi, > > I have been using arrayQualityMetrics, and find it very useful. > However, to make it even more useful, would it be possible to have > legends for some of the plots, e.g. density/ecdf, RNAdeg incorporated in > the output? > > Cheers and thanks, > > a > > > >> sessionInfo() >> > R version 2.6.0 (2007-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] grid splines tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 > simpleaffy_2.14.05 > [5] affyPLM_1.14.0 gcrma_2.10.0 > matchprobes_1.10.0 RColorBrewer_1.0-2 > [9] vsn_3.2.1 limma_2.12.0 affy_1.16.0 > preprocessCore_1.0.0 > [13] affyio_1.6.1 genefilter_1.16.0 survival_2.34 > geneplotter_1.16.0 > [17] lattice_0.17-2 annotate_1.16.1 xtable_1.5-2 > AnnotationDbi_1.0.6 > [21] RSQLite_0.6-4 DBI_0.2-4 Biobase_1.16.1 > > > loaded via a namespace (and not attached): > [1] KernSmooth_2.22-21 > > > > > >
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Hi Audrey, Thanks for the prompt reply. I take your point about split.plots, although sometimes it IS useful to see everything together! Could the html report perhaps have a separate graphic with the legend, which might thus get around the "space on the plot" issue? Cheers and thanks, a > -----Original Message----- > From: audrey [mailto:audrey at ebi.ac.uk] > Sent: 19 December 2007 09:03 > To: Al Ivens > Cc: 'bioc' > Subject: Re: [BioC] arrayQualityMetrics > > > Hi Al, > > Thank you for the useful feedback. In the development version of > arrayQualityMetrics, I have added a legend with the name of the > experiments on the density and ecdf plots. I will think about > adding the > same on the RNAdeg plot in the next version. > However when there are too many experiments there is not > enough place on > the plot to write all the experiment names so I advice you in > that case > to use the argument "split.plots" of arrayQualityMetrics and > to set it > at 20 maximum. > > Thank you, > Audrey > > > Al Ivens wrote: > > Hi, > > > > I have been using arrayQualityMetrics, and find it very useful. > > However, to make it even more useful, would it be possible to have > > legends for some of the plots, e.g. density/ecdf, RNAdeg > incorporated > > in the output? > > > > Cheers and thanks, > > > > a > > > > > > > >> sessionInfo() > >> > > R version 2.6.0 (2007-10-03) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > > Kingdom.1252;LC_MONETARY=English_United > > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] grid splines tools stats graphics > grDevices utils > > datasets methods base > > > > other attached packages: > > [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 > > simpleaffy_2.14.05 > > [5] affyPLM_1.14.0 gcrma_2.10.0 > > matchprobes_1.10.0 RColorBrewer_1.0-2 > > [9] vsn_3.2.1 limma_2.12.0 affy_1.16.0 > > preprocessCore_1.0.0 > > [13] affyio_1.6.1 genefilter_1.16.0 > survival_2.34 > > geneplotter_1.16.0 > > [17] lattice_0.17-2 annotate_1.16.1 > xtable_1.5-2 > > AnnotationDbi_1.0.6 > > [21] RSQLite_0.6-4 DBI_0.2-4 > Biobase_1.16.1 > > > > > > loaded via a namespace (and not attached): > > [1] KernSmooth_2.22-21 > > > > > > > > > > > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
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Hi Al, Nice suggestion, I am still looking for a nice way to present these density plots with the names. So I will think about it with your suggestion. Cheers, Audrey Al Ivens wrote: > Hi Audrey, > > Thanks for the prompt reply. I take your point about split.plots, > although sometimes it IS useful to see everything together! Could the > html report perhaps have a separate graphic with the legend, which might > thus get around the "space on the plot" issue? > > Cheers and thanks, > > a > > >> -----Original Message----- >> From: audrey [mailto:audrey at ebi.ac.uk] >> Sent: 19 December 2007 09:03 >> To: Al Ivens >> Cc: 'bioc' >> Subject: Re: [BioC] arrayQualityMetrics >> >> >> Hi Al, >> >> Thank you for the useful feedback. In the development version of >> arrayQualityMetrics, I have added a legend with the name of the >> experiments on the density and ecdf plots. I will think about >> adding the >> same on the RNAdeg plot in the next version. >> However when there are too many experiments there is not >> enough place on >> the plot to write all the experiment names so I advice you in >> that case >> to use the argument "split.plots" of arrayQualityMetrics and >> to set it >> at 20 maximum. >> >> Thank you, >> Audrey >> >> >> Al Ivens wrote: >> >>> Hi, >>> >>> I have been using arrayQualityMetrics, and find it very useful. >>> However, to make it even more useful, would it be possible to have >>> legends for some of the plots, e.g. density/ecdf, RNAdeg >>> >> incorporated >> >>> in the output? >>> >>> Cheers and thanks, >>> >>> a >>> >>> >>> >>> >>>> sessionInfo() >>>> >>>> >>> R version 2.6.0 (2007-10-03) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United >>> Kingdom.1252;LC_MONETARY=English_United >>> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 >>> >>> attached base packages: >>> [1] grid splines tools stats graphics >>> >> grDevices utils >> >>> datasets methods base >>> >>> other attached packages: >>> [1] arrayQualityMetrics_1.2.0 latticeExtra_0.3-1 CCl4_1.0.6 >>> simpleaffy_2.14.05 >>> [5] affyPLM_1.14.0 gcrma_2.10.0 >>> matchprobes_1.10.0 RColorBrewer_1.0-2 >>> [9] vsn_3.2.1 limma_2.12.0 affy_1.16.0 >>> preprocessCore_1.0.0 >>> [13] affyio_1.6.1 genefilter_1.16.0 >>> >> survival_2.34 >> >>> geneplotter_1.16.0 >>> [17] lattice_0.17-2 annotate_1.16.1 >>> >> xtable_1.5-2 >> >>> AnnotationDbi_1.0.6 >>> [21] RSQLite_0.6-4 DBI_0.2-4 >>> >> Biobase_1.16.1 >> >>> loaded via a namespace (and not attached): >>> [1] KernSmooth_2.22-21 >>> >>> >>> >>> >>> >>> >>> > > > > >
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