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 <http://media.affymetrix.com/support/developer/powertools/changelog/apt-copynumber-onco-ssa.html> 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? Il giorno lunedì 10 luglio 2017 23:05:55 UTC+2, Keith C ha scritto: > > its actually under Convert.. > > From: Andrea O'Hara <aoh...@biodiscovery.com <javascript:>> > Date: Thursday, November 12, 2015 11:35 AM > To: Keith Ching <keith...@pfizer.com <javascript:>>, "Foos, Jonathon" < > jonath...@affymetrix.com <javascript:>> > > 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 <javascript:>] > Sent: Wednesday, November 11, 2015 4:42 PM > To: Foos, Jonathon <jonath...@affymetrix.com <javascript:>>; Andrea > O'Hara <aoh...@biodiscovery.com <javascript:>> > > 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 <keith...@gmail.com <javascript:> > > 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 <mba...@gmail.com >> <javascript:>> 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...@gmail.com <javascript:>> 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. >>>>> > >>>>> > -- >>>>> > -- >>>>> > 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/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-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 "aroma.affymetrix" group with website >>>> http://www.aroma-project.org/. >>>> To post to this group, send email to aroma-af...@googlegroups.com >>>> <javascript:> >>>> To unsubscribe and other options, go to >>>> http://www.aroma-project.org/forum/ >>>> >>>> --- >>>> You received this message because you are subscribed to a topic in the >>>> Google Groups "aroma.affymetrix" group. >>>> To unsubscribe from this topic, visit >>>> https://groups.google.com/d/topic/aroma-affymetrix/Wez3wL1abiA/unsubscribe >>>> . >>>> To unsubscribe from this group and all its topics, send an email to >>>> aroma-affymetr...@googlegroups.com <javascript:>. >>>> 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 "aroma.affymetrix" group with website >>> http://www.aroma-project.org/. >>> To post to this group, send email to aroma-af...@googlegroups.com >>> <javascript:> >>> To unsubscribe and other options, go to >>> http://www.aroma-project.org/forum/ >>> >>> --- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "aroma.affymetrix" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/aroma-affymetrix/Wez3wL1abiA/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, send an email to >>> aroma-affymetr...@googlegroups.com <javascript:>. >>> 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 "aroma.affymetrix" group with website >>> http://www.aroma-project.org/. >>> To post to this group, send email to aroma-af...@googlegroups.com >>> <javascript:> >>> To unsubscribe and other options, go to >>> http://www.aroma-project.org/forum/ >>> >>> --- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "aroma.affymetrix" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/aroma-affymetrix/Wez3wL1abiA/unsubscribe >>> . >>> To unsubscribe from this group and all its topics, send an email to >>> aroma-affymetr...@googlegroups.com <javascript:>. >>> 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. 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