Dear All at BioC, I have used the LD function a lot of times. However it does not seem to work in today's session. I am copying the outputs as well as the sessionInfo(). Any suggestions. --analabha > ld <- LD(MX_US) Error in UseMethod("LD", g1) : no applicable method for "LD" > > > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] fbat_1.6.0 GeneticsPed_1.4.0 genetics_1.3.4 [4] MASS_7.2-45 GeneticsDesign_1.10.0 gtools_2.5.0 [7] gmodels_2.14.1 gdata_2.4.2 GeneticsBase_1.8.0 [10] haplo.stats_1.3.8 mvtnorm_0.9-3 xtable_1.5-4 [13] combinat_0.0-6 loaded via a namespace (and not attached): [1] gplots_2.6.0 tools_2.8.1 [[alternative HTML version deleted]]

Hi Basu, Basu, Analabha wrote: > Dear All at BioC, > > I have used the LD function a lot of times. However it does not seem to > work in today's session. > I am copying the outputs as well as the sessionInfo(). Your sessionInfo() indicates that you are not using the current release of R + Bioconductor. Since we don't support old releases, I highly recommend that you upgrade your installation (R-2.9.0 + BioC 2.4 is the current release). There are 2 LD() functions: one defined in the genetics package, and the other one defined in the GeneticsBase package. By default you get the former (because genetics comes first in your search() path). If you want the latter, please use fully qualified names e.g. GeneticsBase::LD() Maybe in the past you didn't have this symbol masking issue because either genetics was not on your way or it didn't have the LD() function... Cheers, H. > > Any suggestions. > > > --analabha > > >> ld <- LD(MX_US) > Error in UseMethod("LD", g1) : no applicable method for "LD" >> >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] fbat_1.6.0 GeneticsPed_1.4.0 genetics_1.3.4 > [4] MASS_7.2-45 GeneticsDesign_1.10.0 gtools_2.5.0 > [7] gmodels_2.14.1 gdata_2.4.2 GeneticsBase_1.8.0 > [10] haplo.stats_1.3.8 mvtnorm_0.9-3 xtable_1.5-4 > [13] combinat_0.0-6 > > loaded via a namespace (and not attached): > [1] gplots_2.6.0 tools_2.8.1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Thanks Herve, I did just that and it seems to work. Though i am no longer using a MS Windows Vista, but a linux. Thanks again, --a -----Original Message----- From: Hervé Pagès [mailto:hpages@fhcrc.org] Sent: Thu 5/21/2009 11:09 AM To: Basu, Analabha Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] no applicable method for "LD" Hi Basu, Basu, Analabha wrote: > Dear All at BioC, > > I have used the LD function a lot of times. However it does not seem to > work in today's session. > I am copying the outputs as well as the sessionInfo(). Your sessionInfo() indicates that you are not using the current release of R + Bioconductor. Since we don't support old releases, I highly recommend that you upgrade your installation (R-2.9.0 + BioC 2.4 is the current release). There are 2 LD() functions: one defined in the genetics package, and the other one defined in the GeneticsBase package. By default you get the former (because genetics comes first in your search() path). If you want the latter, please use fully qualified names e.g. GeneticsBase::LD() Maybe in the past you didn't have this symbol masking issue because either genetics was not on your way or it didn't have the LD() function... Cheers, H. > > Any suggestions. > > > --analabha > > >> ld <- LD(MX_US) > Error in UseMethod("LD", g1) : no applicable method for "LD" >> >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] fbat_1.6.0 GeneticsPed_1.4.0 genetics_1.3.4 > [4] MASS_7.2-45 GeneticsDesign_1.10.0 gtools_2.5.0 > [7] gmodels_2.14.1 gdata_2.4.2 GeneticsBase_1.8.0 > [10] haplo.stats_1.3.8 mvtnorm_0.9-3 xtable_1.5-4 > [13] combinat_0.0-6 > > loaded via a namespace (and not attached): > [1] gplots_2.6.0 tools_2.8.1 > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319