Hi,

in case I never replied - sorry for *my* delay on saying "no worries"
(I am just trying to get users to address their questions/issues to
the correct receipients).

Cheers,

/Henrik

On Thu, Feb 9, 2012 at 7:59 PM, Roger <rpi...@gmail.com> wrote:
> Dear Henrik and Zelha,
>
> I'm sorry I have not been able to keep up porting GADA to the latest
> versions of aroma.affymetrix. I also apologize for not having been
> able to respond any of the messages you may have sent me. But please,
> send the message again if you need an answer, you can email me at:
> "rpique[AT]uchicago[DOT]edu". Some of my other email adresses may no
> longer work.
>
> Since my research has shifted from copy number, it has been very hard
> for me to keep up maintaining the GADA software specially within
> aroma.affymetrix. I am interested in fixing this because I want to
> make it available to as many people as possible but at the same time
> it will take me a little bit to fix this. Henrik, do you have a
> suggestion on how I could fix it quickly? and also make it easy to
> port to newer versions of aroma.affymetrix.
>
> Best regards and I apologize again for the inconvenience.
>
> Roger
>
> On Dec 31 2011, 7:38 am, Zelha Nil <zelh...@gmail.com> wrote:
>> Thanks Henrik. I ran CRMAv2 and CBS successfully many times. There is
>> nothing wrong with aroma vignettes. Also, I have tried  calmate on my data.
>> Since my data included pairs, I have also performed tumorboost. The aim of
>> my study, as I said earlier, is to find a suitable method for FFPE samples.
>> Till now, I have got only two succesful results among 10 pairs with
>> tumorboost and calmate. For this reason I am trying to run VN method. I
>> also performed PSCBS and I also obtained results for all of the samples.
>> But the thing that I could not understand is that is there a way that we
>> can use TB normalized or Calmate normalized totalandfracB data with PSCBS?
>> From the viignettes I have understood that we should run ASCRMAv2 and after
>> that it uses plm data to obtain CN states and gives the result. Then, what
>> is the point of TB rather than more precise change point detection?
>>
>> Also, I wonder if is there a method to obtain heatmaps of the regions that
>> we obtained after CBS?
>>
>> Also, my other question is that does PSCBS only give result of all
>> chromosomes together or can we obtain each chromosome result separately?
>> Also, I want to obtain DH, TCN, BAF values, can we write them on a xls file
>> after PSCBS?
>>
>> Thank you in advance...
>>
>> Happy new year :)
>>
>> 2011/12/31 Henrik Bengtsson <henrik.bengts...@aroma-project.org>
>>
>>
>>
>>
>>
>>
>>
>> > Hi Zehla,
>>
>> > this is most likely yet another thing caused by the fact that their
>> > code overrides the methods of aroma.affymetrix.  It is simply too
>> > painful trying to troubleshoot what is going wrong when also loading
>> > their orphaned code which overwrites part of aroma.affymetrix.  I
>> > might be able to find another patch like last time, but however much I
>> > wish to help you get through with your project, I'm not too keen
>> > spending time trying to patch their code (I've been there too many
>> > times already), even less so when they are not responding to either
>> > your or me. Their silence strongly suggests that they've orphaned the
>> > method/code and trying to get such to work is not fun and it often
>> > result in having to rewrite everything from scratch.
>>
>> > I recommend that you first make sure you can run CRMAv2 and CBS in
>> > aroma.affymetrix *without* loading any of their code/scripts.  That
>> > asserts that you are using the correct annotation data etc.  So, make
>> > sure you can do:
>>
>> > 1. CRMAv2, e.g.http://aroma-project.org/vignettes/CRMAv2
>> > 2. CBS, e.g.http://aroma-project.org/vignettes/NonPairedCBS
>>
>> > If that is giving you the same error, then there is something wrong
>> > with aroma.affymetrix that needs to be fixed.
>>
>> > Cheers,
>>
>> > Henrik
>>
>> > On Thu, Dec 29, 2011 at 9:55 PM, Zelha Nil <zelh...@gmail.com> wrote:
>> > > Hi Henrik,
>>
>> > > In the method I am using there is a problem again, and I could not find
>> > any
>> > > solution.
>>
>> > >> sessionInfo()
>> > > R version 2.14.0 (2011-10-31)
>> > > Platform: i386-pc-mingw32/i386 (32-bit)
>> > > locale:
>> > > [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> > > States.1252    LC_MONETARY=English_United States.1252
>> > > [4] LC_NUMERIC=C                           LC_TIME=English_United
>> > > States.1252
>> > > attached base packages:
>> > > [1] stats     graphics  grDevices datasets  utils     methods   base
>> > > other attached packages:
>> > >  [1] Cairo_1.5-0            RColorBrewer_1.0-5     signal_0.7-1
>> > > MASS_7.3-16            gada_0.8-5             aroma.affymetrix_2.3.0
>> > >  [7] affxparser_1.26.1      aroma.apd_0.2.0        R.huge_0.3.0
>> > > aroma.core_2.3.2       aroma.light_1.22.0     matrixStats_0.4.0
>> > > [13] R.rsp_0.7.0            R.cache_0.5.2          R.filesets_1.1.3
>> > > digest_0.5.1           R.utils_1.9.6          R.oo_1.8.3
>> > > [19] R.methodsS3_1.2.1
>> > > loaded via a namespace (and not attached):
>> > > [1] tools_2.14.0
>>
>> > > Warning message:
>> > > In method(static, ...) :
>> > >   Ghostscript not found. Searched directories: C:/gs, C:\Program
>> > Files/gs,
>> > > /gs, C:\Program Files\Common Files/gs
>> > >> getSummaryTableFromFile(segModel,"All")
>> > > Reading regions from file...
>> > > Reading genes from file...
>> > > [1] "2011-12-29 22:17:09 EET"
>> > > Error in getSummaryTableFromFile.CopyNumberSegmentationModel(segModel,  :
>> > >   argument "chromosomes" is missing, with no default
>>
>> > > I could not understand why it cannot find chromosomes?? The author of the
>> > > article still has not respond to my mail. If you can help me, I would
>> > > appreciate it.
>>
>> > > Thanx.
>>
>> > > 17 Aralık 2011 13:12 tarihinde Zelha Nil <zelh...@gmail.com> yazdı:
>>
>> > >> Hi Henrik,
>>
>> > >> The "rm" trick helped me :) it worked and I got the xls file. However, I
>> > >> found out that only one tumor or test sample could be used at each
>> > time.I
>> > >> had to change my data structure accordingly.
>>
>> > >> Thanks so much ..
>>
>> > >> Zelha Nil
>>
>> > >> 2011/12/16 Henrik Bengtsson <henrik.bengts...@aroma-project.org>
>>
>> > >>> Hi.
>>
>> > >>> On Fri, Dec 16, 2011 at 3:16 AM, Zelha Nil <zelh...@gmail.com> wrote:
>> > >>> > I have contacted the authors about the problems many times but they
>> > did
>> > >>> > not
>> > >>> > return me. Because of that, I tried to contact you.
>>
>> > >>> I'm sorry to here.  I've found the name "Alex" in the source code
>> > >>> comments, which I guess is first author Alex Lisovich (who has also
>> > >>> been
>> > >>> posting to this list in the past).  I've cc him to see if I can bump
>> > >>> up this issue.
>>
>> > >>> TECHNICAL: The approach that was taken in this "extension" was to
>> > >>> cut'n'paste, "tune" and overwrite existing GADA and aroma.affymetrix
>> > >>> code, which makes it much less agile for changes in underlying
>> > >>> packages.  A bigger concern is that this approach is very likely to
>> > >>> work with R v2.14.0 and beyond, because since then it is much harder
>> > >>> to overwrite existing code (due to so called namespaces).  Alex, if
>> > >>> you read this, I'm happy to guide to do make your code more
>> > >>> sustainable (by basically extending the classes of aroma.affymetrix in
>> > >>> an object-oriented fashion instead of adjusting their code).
>>
>> > >>> My guesstimate is that the error you observe started to appear with
>> > >>> aroma.affymetrix v2.2.0 (April 2011).  Note that this is not a
>> > >>> bug/problem with aroma.affymetrix, only with the "extension".
>> > >>> Unfortunately, it is rather common that published methods are
>> > >>> implemented once and not maintained.  There are lots of reasons for
>> > >>> this, and there is a risk that the method you are trying to use is
>> > >>> one.  If this is not the case here, I would have expected to authors
>> > >>> to have updated their code, because they will also run into this
>> > >>> problem each time they use their method.
>>
>> > >>> The best way to get their scripts working is to use an R version
>> > >>> before R v2.14.0 and install aroma.affymetrix v2.1.0 or before.  That
>> > >>> is not a fun task to do, and I don't recommend it to anyone.
>>
>> > >>> > I did what you said. I deleted the files and run the program.
>> > Actually,
>> > >>> > after doing CRMAv2 we had to change the settings into aromadefault by
>> > >>> > using
>> > >>> > ">settings<-aromaDefaultSettings();". Then ı have run ref generation
>> > >>> > and
>> > >>> > segmentation. However, during report generation there was an error.
>> > >>> > (Error
>> > >>> > in paste("'", chromosomeLabels, "'", sep = "", collapse = ", ") :
>> > >>> >   object 'chromosomeLabels' not found) I made it red below. How can
>> > you
>> > >>> > explain this?
>>
>> > >>> See if the following rm() "trick" will make it work:
>>
>> > >>> setupAromaExtensions();
>> > >>> rm(updateSamplesFile.ChromosomeExplorer);
>>
>> > >>> Then continue "as usual".
>>
>> > >>> If you still run into problems, you could at least try to write the
>> > >>> regions file manually, by:
>>
>> > >>> segModel <- aromaSegmentation(ces1,ref,settings,verbose);
>> > >>> writeRegions(segModel, verbose=verbose);
>>
>> > >>> Now to what you're trying to achieve; if your CN data look really poor
>> > >>> ("noisy", "jumpy", "lots of aberrations all of the place", ...), it is
>> > >>> often due to low quality samples or a bad assay run.  In such cases,
>> > >>> it is unlikely that an statistical method can rescue the true
>> > >>> biological signal.  One can do a little bit, but don't expect magic.
>>
>> > >>> Hope this helps you go forward. Good luck with your thesis.
>>
>> > >>> /Henrik
>>
>> > >>> >> res<-aromaReports(segModel,"TEST",settings,verbose)
>> > >>> > 20111216 13:09:34|Generating ChromosomeExplorer report...
>> > >>> > 20111216 13:09:34| Setting up ChromosomeExplorer report files...
>> > >>> > 20111216 13:09:34|  Copying template files...
>> > >>> > 20111216 13:09:34|   Source path:
>>
>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/includes
>> > >>> > 20111216 13:09:34|   Destination path: reports/includes
>> > >>> > 20111216 13:09:35|  Copying template files...done
>> > >>> > 20111216 13:09:35| Setting up ChromosomeExplorer report files...done
>> > >>> > 20111216 13:09:35| Copying ChromosomeExplorer.html...
>> > >>> > 20111216 13:09:35|  Source pathname:
>>
>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/templates/h
>> >  tml/ChromosomeExplorer/ChromosomeExplorer.html
>> > >>> > 20111216 13:09:35|  Destination pathname:
>>
>> > reports/TEST/ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY,a0.2,paired/ChromosomeExplorer
>> >  .html
>> > >>> > 20111216 13:09:35| Copying ChromosomeExplorer.html...done
>> > >>> > 20111216 13:09:35| Explorer output version: 3
>> > >>> > 20111216 13:09:35| Compiling ChromosomeExplorer.onLoad.js.rsp...
>> > >>> > 20111216 13:09:35|  Source:
>>
>> > C:/Users/bidbid/Documents/R/win-library/2.14/aroma.core/reports/templates/r
>> >  sp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>> > >>> > 20111216 13:09:36|  Output path:
>> > >>> > reports/TEST/ACC,-XY,BPN,-XY,RMA,A+B,FLN,-XY,a0.2,paired
>> > >>> > 20111216 13:09:36|  Scanning directories for available chip types...
>> > >>> > 20111216 13:09:36|   Detected chip types: Mapping250K_Sty
>> > >>> > 20111216 13:09:36|  Scanning directories for available chip
>>
>> ...
>>
>> read more »
>
> --
> 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/

-- 
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/

Reply via email to