[BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth

[Koen Marien]

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 at 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
>
>
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>
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