[BioC] arrayQualityMetrics: Binning grid too coarse for current (small) bandwidth
florian at eldopa.net
Wed Mar 31 23:37:22 CEST 2010
Great, thanks a bunch!
How is India and the new job? And are you planning to come to Seattle
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>
>> 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.
>> 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
>>>> was not able to reproduce these warnings so far, which makes it
>>>> 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
>>> implementation of the 'smoothScatter' function in the 'graphics'
>>> which uses 'image'. It should be possible to replace this with
>>> - I'll see whether I find time to do this; or it would be great if
>>> were keen to provide a patch!
>>> Best wishes
>>> Wolfgang Huber
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