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