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.
Best
Steve McKinney
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
smckinney at bccrc.ca
Steven McKinney wrote:
>
> 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.
Sean
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
--
------------------------------------------------------------------
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
Steven McKinney wrote:
>
> 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.
>
I might have one or two scripts that might be of use. :)
I have a wrapper package for DNAcopy that loads the ratio files and
allows you to pass along parameters to the DNAcopy's segment function.
Contact me off-list if you're interested.
Todd
--
Todd Richmond, PhD
Manager of Research Informatics
NimbleGen Systems, Inc
Madison, WI 53719
1-608-218-7600
