[BioC] Methylation status using lumi

[Richard Mc Eachin]

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 at umich.edu  (734) 998-9249
NCRC, 2800 Plymouth Road
Building 10, Room A121
Ann Arbor, MI 48109-2800


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