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

[Florian Hahne]

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
>>>
>>>
>>
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