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
>
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>



-- 
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>

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