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/
