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

Deepayan Sarkar deepayan.sarkar at gmail.com
Fri Mar 26 12:31:16 CET 2010

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

Now that R 2.11 is around the corner, I will soon release a lattice
update with the raster version.


> 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
>> 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

More information about the Bioconductor mailing list