[BioC] spotSegmentation

[Jason Skelton]

Hi

I'm attempting to use the spotSegmentation package and I've run the demo 
using the dataset provided with the package with no problems.
However its not clear how to use your own images which I'm presuming 
will be tiff images for each channel ?
Also after you have used the spotseg function you can summarize the data 
and receive
foreground & background (median & mean) for each channel.

I'm presuming you extract the background from the foreground for which 
ever you feel appropriate ?
and then use this data from subsequent analysis ?

I'd like to also know what the most appropriate way of dealing with 
NA's  is (presumable the "non-found" spots)
where the spots  in question are printed in duplicate on the array and 
only one of which is "found".

I'm using limma for analysis of data, so I presume I can easily convert 
this data into MA objects ?

Many thanks

Jason

-- 
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Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919