Nexus outputs the probe positions and intensities as well as the
segmentation data.
Just export it as text tables if you want to mine the whole data. Agreed,
looking at one gene at a time is a waste.
But now you need to figure out how to do it for 50K arrays since,
inexplicably, you have to process it one array at a time..
segments.txt has chr, start, end and value
probes.txt has the value for the individual positions.
On Mon, Jul 10, 2017 at 1:10 PM, Michael Baudis <mbau...@gmail.com> wrote:
> Affy recommended to use Nexus software. To generate CNV plots, I used the
> probe level output from Nexus.
>
>
> That (generating plots) is not the point; though I am all for nice CNV
> plots (ahem, arraymap.org), these have no use for data
> mining/meta-analyses etc.
>
> I had Affymetrix representatives in my office showing me plots of our
> Oncoscan data, w/o any idea how to extract probe/segment specific values.
> And, while conversing with many colleagues, nobody knows, either.
>
> So, for us: We're having cancer profiling raw data from a series of rare
> diseases, which is rotting since we have no way of extracting genome mapped
> raw intensities / segmentation calls etc. And we're running a resource with
> >50000 cancer CNA profiles/datasets - but none of them Oncoscan (damned be
> thy name).
>
> Michael.
>
>
> -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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