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

Wolfgang Huber huber at ebi.ac.uk
Sun Jun 18 11:00:09 CEST 2006

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.

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

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