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]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
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> >
>
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>
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