Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
its actually under Convert..
From: Andrea O'Hara
Date: Thursday, November 12, 2015 11:35 AM
To: Keith Ching , "Foos, Jonathon" <
jonathon_f...@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.ch...@pfizer.com]
Sent: Wednesday, November 11, 2015 4:42 PM
To: Foos, Jonathon ; 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
On Mon, Jul 10, 2017 at 1:49 PM, Keith C wrote:
> 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 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
>> >5 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.affymetr
Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
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 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
> >5 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 wrote:
>>> > the CEL files are generated from two separate chips and hybs.
>>> >
>>> > --
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>> > version of the package, 2) to report the output of sessionInfo() and
>>> > traceback(), and 3) to post a complete code example.
>>> >
>>> >
>>> > You received this message because you are subscribed to the Google
>>> Groups
>>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> > To post to this group, send email to aroma-af...@googlegroups.com
>>> > To unsubscribe and other options, go to http://www.aroma-project.org/f
>>> orum/
>>> >
>>> > ---
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>>> > email to aroma-affymetr...@googlegroups.com.
>>> > For more options, visit https://groups.google.com/d/optout.
>>>
>>
>> --
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
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>> To post to this group, send email to aroma-affymetrix@googlegroups.com
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>> orum/
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>&
Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
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 wrote:
>> > the CEL files are generated from two separate chips and hybs.
>> >
>> > --
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to aroma-af...@googlegroups.com
>> > To unsubscribe and other options, go to http://www.aroma-project.org/f
>> orum/
>> >
>> > ---
>> > You received this message because you are subscribed to the Google
>> Groups
>> > "aroma.affymetrix" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an
>> > email to aroma-affymetr...@googlegroups.com.
>> > For more options, visit https://groups.google.com/d/optout.
>>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files
the CEL files are generated from two separate chips and hybs. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] Re: Affymetrix Oncoscan library files
>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. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
[aroma.affymetrix] Re: Affymetrix Oncoscan library files
Hi, did you ever figure out how to process Oncoscan arrays using aroma? thanks, -keith On Monday, September 15, 2014 at 4:11:50 AM UTC-7, mbaudis wrote: > > 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. > -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
