Affymetrix Oncoscan library files

[mbaudis]

Hi,

has anybody processed Affymetrix Oncoscan arrays in aroma, and has generated the relevant CDF ... files?

http://www.affymetrix.com/catalog/131419/AFFY/OncoScan+FFPE+Assay+Kit#1_3

Thanks,

Michael. 

[Keith C]

Hi,

did you ever figure out how to process Oncoscan arrays using aroma?

thanks,

-keith

[Henrik Bengtsson]

I don't know anything about the OncoScan assay, but from looking at

http://www.affymetrix.com/catalog/131419/AFFY/OncoScan%26%23174%3B+FFPE+Assay+Kit#1_3

it doesn't look like it's a classical Affymetrix chip. Basically, if
CEL files are not produced, then Aroma almost certainly won't be able
to process the data. Also, almost everything in Aroma requires a CDF,
so unless a CDF can be obtained or created, that is also a show
stopped.

My $.02

/Henrik

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[Keith C]

From what I understand, the OncoScan assay has a different capture method but in the end still involves hybridization to probes on a chip.
The output is two CEL files, A and C which represent AT and GC.  Using their oncoscan software, it combines the two CEL files into a .OSCHP file
which you can process with DNA Nexus.  One advantage is that they have precharacterized normal diploid cells so that a hapmap reference sample is
no longer required.  However, the process is a pain and involves a lot of manual interface clicking, file matching, and manual generation of images.
I have not found a way to simply export the segmentation data.  I was told by Affy that OncoScan does not use a CDF file, but rather a PGR.CLF file.  I'm trying
to get a hold of one to see what the difference is and if its convertable into CDF format.

What I mainly want is a chromosome explorer type output of
1. images of all chromosomes for all samples.  (that's 24 plots by hand per sample using Nexus )
2. segmentation file including non-cnv altered segments.  Currently Nexus only outputs regions of significance.

[Michael Baudis]

This doesn't sound good. It makes Oncoscan unusable for research projects.

Michael.

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[Henrik Bengtsson]

Actually, if there are regular CEL files outputted, and assuming
they're not non-supported multi-channel CEL files, then it might not
be an impossible task. There is still a need for a CDF though, but
people have built CDF for Affymetrix chiptypes that don't official
have CDFs.

First question that comes to mind is whether the two CEL files are
coming from a single hybridization/chip, or two separate
hybridizations/chips. If from a single one, then one could imagine
creating a virtual chip where one start by merging the data from the
two CEL files into one bigger CEL file. Likewise, one can then create
one CDF file for this virtual file. From there, low-level affxparser
should be able to parse both the CEL and the CDF just as for any
regular chip type.

This are just the first few baby-step thoughts, but it is possible
that this chip type could be brought into the Aroma framework with
some work.

/Henrik

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[Keith C]

the CEL files are generated from two separate chips and hybs.

[Henrik Bengtsson]

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.
>

[Francesca Scellato]

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.

[Keith C]

Affy recommended to use Nexus software.  To generate CNV plots, I used the probe level output from Nexus.

-keith

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[Michael Baudis]

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.

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[Keith C]

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.

[Keith C]

its actually under Convert..

From: Andrea O'Hara <aoh...@biodiscovery.com>
Date: Thursday, November 12, 2015 11:35 AM
To: Keith Ching <Keith...@pfizer.com>, "Foos, Jonathon" <Jonath...@affymetrix.com>

Subject: RE: Affymetrix Oncoscan bioinformatics - follow up 1.

Hi Keith,
 
Thank you for your patience.  Regarding the segment values, there is a tool in the menu File>Utilities>Convert .ivg to .txt that will generate a separate segments.txt file for each sample which contains the probe segment coordinates and LogR values for every segment in the selected samples.
 
With regards to the pictures, unfortunately there is currently no automated way to generate those pictures. I will pass along this feature request though so that it may be incorporated into a future version of the software.
 
With regards to the error message, this typically indicates a discrepancy with your genome build. Are you sure you using older 36.1 results and loading into the newer 37 genome build? Which chromosome(s) is the error message occurring at? Depending on what the actual issue is there are different solutions for preventing that error message from popping up every time.
 
Please let me know if there is anything else I can assist you with.
Thanks!
Andrea
 
From: Ching, Keith [mailto:Keith...@pfizer.com]
Sent: Wednesday, November 11, 2015 4:42 PM
To: Foos, Jonathon <Jonath...@affymetrix.com>; Andrea O'Hara <aoh...@biodiscovery.com>

Subject: Re: Affymetrix Oncoscan bioinformatics - follow up 1.
 
Hi Andrea,
 
In Nexus 7.5, is there a way to export the segmentation table for every segment, not just the altered ones?
When I go to export the table, it only shows CN Gains, losses, allelic imbalances, etc.. but I need to know
what the probe median value of a segment was, even if its not altered.
 
Also, is there a way to make this plot automatically for each chr, for each sample?  If I have 10 samples, that's 240 plots.. its really tedious.. Can there be a button to export the png for each chr?  I don't mind doing it once per sample.

and everytime it pops an error mesg to tell me that probes are out of range.  can
there be a checkbox to ignore that error mesg so I don't have to click it 240 times?
 
thanks,
 
-keith

[Francesca Scellato]

Thank you all for your answers.

I was able to export from Nexus the segment, probes and snps file for each sample.

I'm still looking for an alternative way to process the CEL files (other that Nexus) that will allow a more personalized analysis; I've come across the Affymetrix Power Tools but I have some problems running the apt-copynumber-onco-ssa command (I have already asked for help).

Now I'm trying to prepare the two files needed to perform the GISTIC analysis.

Has anyone already tried it?

-keith

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