Affy recommended to use Nexus software. To generate CNV plots, I used the
probe level output from Nexus.
-keith
On Mon, Jul 10, 2017 at 6:21 AM, Francesca Scellato <
francesca.scell...@gmail.com> wrote:
> Hi!
> I found online this discussion because I'm looking for the CDF file for
> Oncoscan CNV array.
> I'm new to R and data analysis but everything that I've found so far to
> analyze CEL files requires that CDF file.
>
> Have you managed to find a solution during these past years?
>
> Thank you in advance.
>
> Il giorno sabato 14 novembre 2015 00:15:03 UTC+1, Henrik Bengtsson ha
> scritto:
>>
>> Ok, so that complicates how one would look at the pre-processing and
>> how to normalize the signals, e.g. one should probably normalize probe
>> signals of the two CEL files separately and only merge them after this
>> step.
>>
>> A small first step would be to see if you can create a spatial image
>> of the CEL files, e.g.
>>
>> library("aroma.affymetrix")
>> df <- AffymetrixCelFile("rawData/FusionSDK_Test3/Test3/Test3-1-121502.CEL")
>>
>> print(df)
>>
>> ## Display in R
>> img <- getImage(df)
>> display(img)
>>
>> ## Generate a PNG and view it
>> png <- writeImage(df)
>> browseURL(png)
>>
>> /Henrik
>>
>>
>> On Thu, Nov 12, 2015 at 5:05 PM, Keith C <keith...@gmail.com> wrote:
>> > the CEL files are generated from two separate chips and hybs.
>> >
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