Hello All: I'd like to use the gammaFitEM(), methylationCall( ), and lumiMethyStatus() functions in lumi to distinguish methylated vs. unmethylated sites on HumanMethylation27k chips. I've worked my way up to pg 40 in "Analyze Illumina Infinium methylation microarray data". I downloaded the lumi package fresh today. Here's my command: >fittedGamma <- gammaFitEM(exprs(x.cnorm.bg.qn)[ ,1], plotMode=TRUE) and the error message: Error: could not find function "gammaFitEM" x.cnorm.bg.qn is a MethyLumiM object. Also gammaFitEM is in "http://w ww.bioconductor.org/packages/2.8/bioc/manuals/lumi/man/lumi.pdf" Anyone know what am I missing? Thanks, Rich McEachin ---------------------------------------------------------------------- ---------------- > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] KernSmooth_2.23-4 lumi_2.2.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.1 affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.1 [5] DBI_0.2-5 grid_2.12.2 hdrcde_2.15 lattice_0.19-17 [9] MASS_7.3-11 Matrix_0.999375-46 methylumi_1.6.1 mgcv_1.7-3 [13] nlme_3.1-98 preprocessCore_1.12.0 RSQLite_0.9-4 tools_2.12.2 [17] xtable_1.5-6 > traceback() No traceback available ------------------------------------------ Richard C. McEachin, PhD Research Investigator University of Michigan, Center for Computational Medicine and Bioinformatics mceachin at umich.edu (734) 998-9249 NCRC, 2800 Plymouth Road Building 10, Room A121 Ann Arbor, MI 48109-2800 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

you're running an older version of R. gammaFitEM wasn't in older versions of lumi. you will need to upgrade to Bioconductor 2.8 to use the methylation call functions On Tue, May 10, 2011 at 10:38 AM, Richard Mc Eachin <mceachin@med.umich.edu>wrote: > Hello All: > > I'd like to use the gammaFitEM(), methylationCall( ), and lumiMethyStatus() > functions in lumi to distinguish methylated vs. unmethylated sites on > HumanMethylation27k chips. I've worked my way up to pg 40 in "Analyze > Illumina Infinium methylation microarray data". I downloaded the lumi > package fresh today. Here's my command: > > >fittedGamma <- gammaFitEM(exprs(x.cnorm.bg.qn)[ ,1], plotMode=TRUE) > > and the error message: > > Error: could not find function "gammaFitEM" > > x.cnorm.bg.qn is a MethyLumiM object. Also gammaFitEM is in " > http://www.bioconductor.org/packages/2.8/bioc/manuals/lumi/man/lumi. pdf" > > Anyone know what am I missing? > > Thanks, Rich McEachin > > > -------------------------------------------------------------------- ------------------ > > sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KernSmooth_2.23-4 lumi_2.2.1 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affy_1.28.1 affyio_1.18.0 annotate_1.28.1 > AnnotationDbi_1.12.1 > [5] DBI_0.2-5 grid_2.12.2 hdrcde_2.15 > lattice_0.19-17 > [9] MASS_7.3-11 Matrix_0.999375-46 methylumi_1.6.1 > mgcv_1.7-3 > [13] nlme_3.1-98 preprocessCore_1.12.0 RSQLite_0.9-4 > tools_2.12.2 > [17] xtable_1.5-6 > > > traceback() > No traceback available > > ------------------------------------------ > > Richard C. McEachin, PhD > Research Investigator > University of Michigan, Center for Computational Medicine and > Bioinformatics > mceachin@umich.edu (734) 998-9249 > NCRC, 2800 Plymouth Road > Building 10, Room A121 > Ann Arbor, MI 48109-2800 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- If people do not believe that mathematics is simple, it is only because they do not realize how complicated life is. John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> [[alternative HTML version deleted]]