[BioC] Scripts to handle array CGH data files from NimbleGen

[Wolfgang Huber]

Hi Sean,

>> Before I reinvent the wheel, has anyone set up scripts to read in
>> array CGH data files from NimbleGen, for use in the aCGH package or
>> a similar package?
>>
>> I have normalized NimbleGen files
>> ([array_id]_[identifier]_normalized.txt in the NimbleGen naming scheme)
>> several to a directory, to read in and use to create an aCGH object.
>>
>> Any info appreciated.
> 
> You might want to look at the oligo and tilingArray packages (and maybe 
> others).  If I remember, each can handle nimblegen arrays--the authors 
> can probably be more specific.
> 

the tilingArray package currently does not offer any methods for data 
import of Nimblegen arrays. It might be useful for subsequent 
normalization and segmentation (idenfication of gains/losses), but I 
have no experience with that for Nimblegen data.

Best
-- 
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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber