arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth
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Koen Marien ▴ 50
@koen-marien-3971
Last seen 10.2 years ago
Dear When using the arrayQualityMetrics package on my Affymetrix data, a full report (the .html-file) gets generated but I get these warnings: The directory ### has been created. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] NULL NULL Warning messages: 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' I use R version 2.9.2. Info about the data: AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse430_2 (45101 affyids) number of samples=3 number of genes=45101 annotation=mouse4302 notes= Can I increase the 'gridsize'? The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB, spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs? Regards Koen Marien student Bioscience Engineering: Cell and Gene Biotechnology University of Ghent [[alternative HTML version deleted]]
arrayQualityMetrics arrayQualityMetrics • 5.9k views
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Koen Marien ▴ 30
@koen-marien-3918
Last seen 10.2 years ago
Dear When using the arrayQualityMetrics package on my Affymetrix data, a full report (the .html-file) gets generated but I get these warnings: The directory ### has been created. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) [[1]] NULL NULL Warning messages: 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : Binning grid too coarse for current (small) bandwidth: consider increasing 'gridsize' I use R version 2.9.2. Info about the data: AffyBatch object size of arrays=1002x1002 features (8 kb) cdf=Mouse430_2 (45101 affyids) number of samples=3 number of genes=45101 annotation=mouse4302 notes= Can I increase the 'gridsize'? The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB, spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs? Regards Koen Marien student Bioscience Engineering: Cell and Gene Biotechnology University of Ghent [[alternative HTML version deleted]]
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@audrey-kauffmann-3982
Last seen 10.2 years ago
Dear Koen, Thank you for your feedback, I will have a look at the warnings you are mentioning. I have seen this before on users machine during tutorials but I was not able to reproduce these warnings so far, which makes it difficult to correct it (I actually thought I corrected it). About the size of the pdf files, what you can do is to use each of the aqm.xxx functions to generate the figures one by one, and then save them with your specifications to make them smaller/lighter. Best wishes, Audrey -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53 2010/3/18 Koen Marien <koen.marien@ugent.be> > Dear > > > > > > When using the arrayQualityMetrics package on my Affymetrix data, a full > report (the .html-file) gets generated but I get these warnings: > arrayqualitymetrics > The directory ### has been created. > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > NULL > > NULL > > Warning messages: > > 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > > > I use R version 2.9.2. Info about the data: > > AffyBatch object > > size of arrays=1002x1002 features (8 kb) > > cdf=Mouse430_2 (45101 affyids) > > number of samples=3 > > number of genes=45101 > > annotation=mouse4302 > > notes= > > > > Can I increase the 'gridsize'? > > The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB, > spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs? > > > > > > Regards > > > > Koen Marien > > student Bioscience Engineering: Cell and Gene Biotechnology > > University of Ghent > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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> Dear Koen, > > Thank you for your feedback, I will have a look at the warnings you are > mentioning. I have seen this before on users machine during tutorials but I > was not able to reproduce these warnings so far, which makes it difficult to > correct it (I actually thought I corrected it). > About the size of the pdf files, what you can do is to use each of the > aqm.xxx functions to generate the figures one by one, and then save them > with your specifications to make them smaller/lighter. I suppose the file size problem eventually traces down to the current implementation of the 'smoothScatter' function in the 'graphics' package, which uses 'image'. It should be possible to replace this with 'grid.raster' - I'll see whether I find time to do this; or it would be great if someone were keen to provide a patch! Best wishes Wolfgang -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber/contact
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Hi Wolfgang, I am not sure that we want to move smoothScatter from base graphics to grid graphics. This makes adding to the graph much harder. There is a grid version in the lattice package using panel.levelplot, so maybe Deepayan can be convinced to use grid.raster directly in there. Bw, Florian On 23.03.2010, at 09:32, Wolfgang Huber wrote: >> Dear Koen, >> Thank you for your feedback, I will have a look at the warnings you >> are >> mentioning. I have seen this before on users machine during >> tutorials but I >> was not able to reproduce these warnings so far, which makes it >> difficult to >> correct it (I actually thought I corrected it). >> About the size of the pdf files, what you can do is to use each of >> the >> aqm.xxx functions to generate the figures one by one, and then save >> them >> with your specifications to make them smaller/lighter. > > > I suppose the file size problem eventually traces down to the > current implementation of the 'smoothScatter' function in the > 'graphics' package, which uses 'image'. It should be possible to > replace this with 'grid.raster' - I'll see whether I find time to do > this; or it would be great if someone were keen to provide a patch! > > > Best wishes > Wolfgang > > > -- > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber/contact > >
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On Wed, Mar 24, 2010 at 1:26 AM, Florian Hahne <florian at="" eldopa.net=""> wrote: > Hi Wolfgang, > I am not sure that we want to move smoothScatter from base graphics to grid > graphics. This makes adding to the graph much harder. There is a grid > version in the lattice package using panel.levelplot, so maybe Deepayan can > be convinced to use grid.raster directly in there. The lattice svn already had an implementation (panel.levelplot.raster), not yet released because grid.raster() is r-devel only (and CRAN doesn't have a devel section, unlike bioc). I have now also added a 'raster=FALSE/TRUE' option to panel.smoothScatter(). Now that R 2.11 is around the corner, I will soon release a lattice update with the raster version. -Deepayan > Bw, > Florian > > > > On 23.03.2010, at 09:32, Wolfgang Huber wrote: > >>> Dear Koen, >>> Thank you for your feedback, I will have a look at the warnings you are >>> mentioning. I have seen this before on users machine during tutorials but >>> I >>> was not able to reproduce these warnings so far, which makes it difficult >>> to >>> correct it (I actually thought I corrected it). >>> About the size of the pdf files, what you can do is to use each of the >>> aqm.xxx functions to generate the figures one by one, and then save them >>> with your specifications to make them smaller/lighter. >> >> >> I suppose the file size problem eventually traces down to the current >> implementation of the 'smoothScatter' function in the 'graphics' package, >> which uses 'image'. It should be possible to replace this with 'grid.raster' >> - I'll see whether I find time to do this; or it would be great if someone >> were keen to provide a patch! >> >> >> Best wishes >> ? ?Wolfgang >> >> >> -- >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber/contact >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Great, thanks a bunch! How is India and the new job? And are you planning to come to Seattle for BioC2010? Cheers, Florian On 26.03.2010, at 12:31, Deepayan Sarkar wrote: > On Wed, Mar 24, 2010 at 1:26 AM, Florian Hahne <florian at="" eldopa.net=""> > wrote: >> Hi Wolfgang, >> I am not sure that we want to move smoothScatter from base graphics >> to grid >> graphics. This makes adding to the graph much harder. There is a grid >> version in the lattice package using panel.levelplot, so maybe >> Deepayan can >> be convinced to use grid.raster directly in there. > > The lattice svn already had an implementation > (panel.levelplot.raster), not yet released because grid.raster() is > r-devel only (and CRAN doesn't have a devel section, unlike bioc). I > have now also added a 'raster=FALSE/TRUE' option to > panel.smoothScatter(). > > Now that R 2.11 is around the corner, I will soon release a lattice > update with the raster version. > > -Deepayan > > >> Bw, >> Florian >> >> >> >> On 23.03.2010, at 09:32, Wolfgang Huber wrote: >> >>>> Dear Koen, >>>> Thank you for your feedback, I will have a look at the warnings >>>> you are >>>> mentioning. I have seen this before on users machine during >>>> tutorials but >>>> I >>>> was not able to reproduce these warnings so far, which makes it >>>> difficult >>>> to >>>> correct it (I actually thought I corrected it). >>>> About the size of the pdf files, what you can do is to use each >>>> of the >>>> aqm.xxx functions to generate the figures one by one, and then >>>> save them >>>> with your specifications to make them smaller/lighter. >>> >>> >>> I suppose the file size problem eventually traces down to the >>> current >>> implementation of the 'smoothScatter' function in the 'graphics' >>> package, >>> which uses 'image'. It should be possible to replace this with >>> 'grid.raster' >>> - I'll see whether I find time to do this; or it would be great if >>> someone >>> were keen to provide a patch! >>> >>> >>> Best wishes >>> Wolfgang >>> >>> >>> -- >>> Wolfgang Huber >>> EMBL >>> http://www.embl.de/research/units/genome_biology/huber/contact >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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Dear all When creating the figures one by one, how can I influence the quality/size of the aqm objects? I can save the figures as jpg's, but I can't get these in the final html report via R I guess? Do I need to edit the html file outside R? Thanks Koen -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Audrey Kauffmann Sent: maandag 22 maart 2010 18:49 To: Koen Marien Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth Dear Koen, Thank you for your feedback, I will have a look at the warnings you are mentioning. I have seen this before on users machine during tutorials but I was not able to reproduce these warnings so far, which makes it difficult to correct it (I actually thought I corrected it). About the size of the pdf files, what you can do is to use each of the aqm.xxx functions to generate the figures one by one, and then save them with your specifications to make them smaller/lighter. Best wishes, Audrey -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53 2010/3/18 Koen Marien <koen.marien at="" ugent.be=""> > Dear > > > > > > When using the arrayQualityMetrics package on my Affymetrix data, a full > report (the .html-file) gets generated but I get these warnings: > arrayqualitymetrics > The directory ### has been created. > > KernSmooth 2.23 loaded > > Copyright M. P. Wand 1997-2009 > > (loaded the KernSmooth namespace) > > [[1]] > > > > NULL > > NULL > > Warning messages: > > 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > Binning grid too coarse for current (small) bandwidth: consider increasing > 'gridsize' > > > > I use R version 2.9.2. Info about the data: > > AffyBatch object > > size of arrays=1002x1002 features (8 kb) > > cdf=Mouse430_2 (45101 affyids) > > number of samples=3 > > number of genes=45101 > > annotation=mouse4302 > > notes= > > > > Can I increase the 'gridsize'? > > The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB, > spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs? > > > > > > Regards > > > > Koen Marien > > student Bioscience Engineering: Cell and Gene Biotechnology > > University of Ghent > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Koen, You can change the options width, height and dpi in the png function when you create the images to influence the size of the figure. To have your figures in the html report, this is really not straightforward because the function aqm.writereport usually creates the png and pdf image files from the aqm objects. You can either edit the html, or you can name your images as they normally are automatically with the aqm.writereport function. You can also write your own modified aqm.writereport function but this is more advanced. Best wishes, Audrey -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53 2010/3/24 Koen Marien <koenmarien87@gmail.com> > Dear all > > When creating the figures one by one, how can I influence the quality/size > of the aqm objects? I can save the figures as jpg's, but I can't get these > in the final html report via R I guess? Do I need to edit the html file > outside R? > > Thanks > > Koen > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Audrey > Kauffmann > Sent: maandag 22 maart 2010 18:49 > To: Koen Marien > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] arrayQualityMetrics: Binning grid too coarse for > current > (small) bandwidth > > Dear Koen, > > Thank you for your feedback, I will have a look at the warnings you are > mentioning. I have seen this before on users machine during tutorials but I > was not able to reproduce these warnings so far, which makes it difficult > to > correct it (I actually thought I corrected it). > About the size of the pdf files, what you can do is to use each of the > aqm.xxx functions to generate the figures one by one, and then save them > with your specifications to make them smaller/lighter. > > Best wishes, > Audrey > > -- > Audrey Kauffmann > Bergonie Cancer Institute > 229 Cours de l'Argonne > 33076 Bordeaux > France > +33.5.56.33.04.53 > > > 2010/3/18 Koen Marien <koen.marien@ugent.be> > > > Dear > > > > > > > > > > > > When using the arrayQualityMetrics package on my Affymetrix data, a full > > report (the .html-file) gets generated but I get these warnings: > > arrayqualitymetrics > > The directory ### has been created. > > > > KernSmooth 2.23 loaded > > > > Copyright M. P. Wand 1997-2009 > > > > (loaded the KernSmooth namespace) > > > > [[1]] > > > > > > > > NULL > > > > NULL > > > > Warning messages: > > > > 1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > 2: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > 3: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > 4: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > 5: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > 6: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) : > > > > Binning grid too coarse for current (small) bandwidth: consider > increasing > > 'gridsize' > > > > > > > > I use R version 2.9.2. Info about the data: > > > > AffyBatch object > > > > size of arrays=1002x1002 features (8 kb) > > > > cdf=Mouse430_2 (45101 affyids) > > > > number of samples=3 > > > > number of genes=45101 > > > > annotation=mouse4302 > > > > notes= > > > > > > > > Can I increase the 'gridsize'? > > > > The pdf's created also have very big sizes (e.g. meansd.pdf: 27.402 KB, > > spatial.pdf: 139.915 KB), is it possible to create smaller sized graphs? > > > > > > > > > > > > Regards > > > > > > > > Koen Marien > > > > student Bioscience Engineering: Cell and Gene Biotechnology > > > > University of Ghent > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
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