R crashes after image array plots hgu133plus2 in R2.6.0
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@richard-friedman-513
Last seen 7.7 years ago
Dear Bioconductor Users. I am trying to do Image array plots of hgu133plus2 chips with the new release of Bioconductor (includiong affy 1.16.0) under R 2.60 on a Mac (10.4) . I am using the command >image(eset[,1]) and I get an image array. But R crashes after the second image. I then tried it with the latest version of R and Bioconductor on my PC, this time with AffylmGUI ( I have not yet got the GUI to work on the Mac, but that is not the problem I am writing about now). R didn't crash but again after 2 images I couldn't get another image. I seemed to remember this operation working properly with earlier versions of R and Bioconductor on the same chip. So I tried it with AffylmGUI 1.5.4 using Limma 2.7.6 unde R 2.31 on the PC. I was just able to get 3 chip images in a row without mishap. So it seems that I am doing something that once worked and now no longer does. Any suggestions would be appreciated. Thanks and best wishes, Rich -------------------------------------------------------- Richard A. Friedman, PhD Biomedical Informatics Shared Resource Lecturer Department of Biomedical Informatics Educational Coordinator Center for Computational Biology and Bioinformatics National Center for Multiscale Analysis of Genomic Networks Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "The last 250 pages of the last Harry Potter book took place in one day because alot happened in that day. All of Ulysses takes place in one day and nothing happened in that day." -Rose Friedman, age 11
GUI hgu133plus2 affy limma affylmGUI GUI hgu133plus2 affy limma affylmGUI • 734 views
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@martin-morgan-1513
Last seen 10 days ago
United States
Hi Richard -- what does sessionInfo() say? My guess (in a bit of rut on this!) is that you need to update packages so that Bioconductor and R agree. See http://www.bioconductor.org/docs/install-howto.html Please report back to the list, and if you do not have success include the output of sessionInfo(). Also provide additional detail about what 'crash' means (R error message? windows error dialog box?) Martin Richard Friedman <friedman at="" cancercenter.columbia.edu=""> writes: > correction to post below: > > I tried > > image(Data[,1]) > > where data was an affybatch object > > Rich > On Oct 31, 2007, at 12:31 PM, Richard Friedman wrote: > >> Dear Bioconductor Users. >> >> I am trying to do Image array plots of hgu133plus2 chips with the >> new release of Bioconductor (includiong affy 1.16.0) >> under R 2.60 on a Mac (10.4) . I am using the command >> >>> image(eset[,1]) >> >> and I get an image array. But R crashes after the second image. >> >> I then tried it with the latest version of R and Bioconductor on >> my PC, >> this time with AffylmGUI ( I have not yet got the GUI to work on the >> Mac, but >> that is not the problem I am writing about now). >> >> R didn't crash but again after 2 images I couldn't get another image. >> >> I seemed to remember this operation working properly with earlier >> versions >> of R and Bioconductor on the same chip. So I tried it with AffylmGUI >> 1.5.4 >> using Limma 2.7.6 unde R 2.31 on the PC. I was just able to get 3 >> chip >> images in a row without mishap. >> >> So it seems that I am doing something that once worked and now >> no longer does. >> >> Any suggestions would be appreciated. >> >> Thanks and best wishes, >> Rich >> -------------------------------------------------------- >> Richard A. Friedman, PhD >> Biomedical Informatics Shared Resource >> Lecturer >> Department of Biomedical Informatics >> Educational Coordinator >> Center for Computational Biology and Bioinformatics >> National Center for Multiscale Analysis of Genomic Networks >> Box 95, Room 130BB or P&S 1-420C >> Columbia University Medical Center >> 630 W. 168th St. >> New York, NY 10032 >> (212)305-6901 (5-6901) (voice) >> friedman at cancercenter.columbia.edu >> http://cancercenter.columbia.edu/~friedman/ >> >> "The last 250 pages of the last Harry Potter >> book took place in one day because alot >> happened in that day. All of Ulysses takes >> place in one day and nothing happened in that day." >> -Rose Friedman, age 11 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Martin and Everybody, Here is a record of the session: > Data<-ReadAffy() > sessionInfo() R version 2.6.0 (2007-10-03) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 [4] Biobase_1.16.1 loaded via a namespace (and not attached): [1] simpleaffy_2.14.05 > image(Data[,1]) #produced image which I closed > image(Data[,2]) #produced image, which I closed > image(Data[,3]) # R disappears and I get an error message that states The application R quit unexpectedly Are you interested in what I see when I click "Report". it is long. THANKS! Rich On Oct 31, 2007, at 2:03 PM, Martin Morgan wrote: > Hi Richard -- > > what does sessionInfo() say? My guess (in a bit of rut on this!) is > that you need to update packages so that Bioconductor and R agree. See > > http://www.bioconductor.org/docs/install-howto.html > > Please report back to the list, and if you do not have success include > the output of sessionInfo(). Also provide additional detail about what > 'crash' means (R error message? windows error dialog box?) > > Martin > > Richard Friedman <friedman at="" cancercenter.columbia.edu=""> writes: > >> correction to post below: >> >> I tried >> >> image(Data[,1]) >> >> where data was an affybatch object >> >> Rich >> On Oct 31, 2007, at 12:31 PM, Richard Friedman wrote: >> >>> Dear Bioconductor Users. >>> >>> I am trying to do Image array plots of hgu133plus2 chips with the >>> new release of Bioconductor (includiong affy 1.16.0) >>> under R 2.60 on a Mac (10.4) . I am using the command >>> >>>> image(eset[,1]) >>> >>> and I get an image array. But R crashes after the second image. >>> >>> I then tried it with the latest version of R and Bioconductor on >>> my PC, >>> this time with AffylmGUI ( I have not yet got the GUI to work on the >>> Mac, but >>> that is not the problem I am writing about now). >>> >>> R didn't crash but again after 2 images I couldn't get another >>> image. >>> >>> I seemed to remember this operation working properly with earlier >>> versions >>> of R and Bioconductor on the same chip. So I tried it with AffylmGUI >>> 1.5.4 >>> using Limma 2.7.6 unde R 2.31 on the PC. I was just able to get 3 >>> chip >>> images in a row without mishap. >>> >>> So it seems that I am doing something that once worked and now >>> no longer does. >>> >>> Any suggestions would be appreciated. >>> >>> Thanks and best wishes, >>> Rich >>> -------------------------------------------------------- >>> Richard A. Friedman, PhD >>> Biomedical Informatics Shared Resource >>> Lecturer >>> Department of Biomedical Informatics >>> Educational Coordinator >>> Center for Computational Biology and Bioinformatics >>> National Center for Multiscale Analysis of Genomic Networks >>> Box 95, Room 130BB or P&S 1-420C >>> Columbia University Medical Center >>> 630 W. 168th St. >>> New York, NY 10032 >>> (212)305-6901 (5-6901) (voice) >>> friedman at cancercenter.columbia.edu >>> http://cancercenter.columbia.edu/~friedman/ >>> >>> "The last 250 pages of the last Harry Potter >>> book took place in one day because alot >>> happened in that day. All of Ulysses takes >>> place in one day and nothing happened in that day." >>> -Rose Friedman, age 11 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/ >>> gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/ >> gmane.science.biology.informatics.conductor
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@richard-friedman-513
Last seen 7.7 years ago
correction to post below: I tried image(Data[,1]) where data was an affybatch object Rich On Oct 31, 2007, at 12:31 PM, Richard Friedman wrote: > Dear Bioconductor Users. > > I am trying to do Image array plots of hgu133plus2 chips with the > new release of Bioconductor (includiong affy 1.16.0) > under R 2.60 on a Mac (10.4) . I am using the command > >> image(eset[,1]) > > and I get an image array. But R crashes after the second image. > > I then tried it with the latest version of R and Bioconductor on > my PC, > this time with AffylmGUI ( I have not yet got the GUI to work on the > Mac, but > that is not the problem I am writing about now). > > R didn't crash but again after 2 images I couldn't get another image. > > I seemed to remember this operation working properly with earlier > versions > of R and Bioconductor on the same chip. So I tried it with AffylmGUI > 1.5.4 > using Limma 2.7.6 unde R 2.31 on the PC. I was just able to get 3 > chip > images in a row without mishap. > > So it seems that I am doing something that once worked and now > no longer does. > > Any suggestions would be appreciated. > > Thanks and best wishes, > Rich > -------------------------------------------------------- > Richard A. Friedman, PhD > Biomedical Informatics Shared Resource > Lecturer > Department of Biomedical Informatics > Educational Coordinator > Center for Computational Biology and Bioinformatics > National Center for Multiscale Analysis of Genomic Networks > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "The last 250 pages of the last Harry Potter > book took place in one day because alot > happened in that day. All of Ulysses takes > place in one day and nothing happened in that day." > -Rose Friedman, age 11 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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