Hello all,

 I am using lumi for the  Illumina methylation microarray data analysis.
Everything went smoothly (background adjustment, color adjustment,
normalization,....) until I tried to use gammaFitEM(), methylationCall( ),
and lumiMethyStatus() functions.

When I run those function in the example.lumiMethy they perform well, so I
guess there is something wrong in my  input data. This is the error I get:
> fileName <- "FinalReportCM.txt"
> mama <- lumiMethyR (fileName, lib="IlluminaHumanMethylation27k.db")
> summary (mama)
    Length      Class       Mode
         1 MethyLumiM         S4

> fittedGamma <- gammaFitEM(exprs(mama)[,1], plotMode=TRUE)

Error in if (abs(p.new[1] - p[1]) < tol) break :
  missing value where TRUE/FALSE needed

> methyCall <- lumiMethyStatus(mama)

Error in if (abs(p.new[1] - p[1]) < tol) break :
  missing value where TRUE/FALSE needed

I printed both the M0<- exprs(mama) and M<-exprs (example.lumiMethy ) out
and I couldn´t spot any difference between them. On the other hand I didn´t
see any NA values in the exprs(mama) data.matrix.

*The data is exported from GenomeStudio version V2010.3.
**
**Thanks for any help,
**
**Naiara*

-- 
-------------------------------------------------------------------------------------------------------------
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] 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] lumi_2.4.0     nleqslv_1.8.3  Biobase_2.12.1
loaded via a namespace (and not attached):
 [1] affy_1.30.0           affyio_1.20.0         annotate_1.30.0
 [4] AnnotationDbi_1.14.1  DBI_0.2-5             grid_2.13.0
 [7] hdrcde_2.15           KernSmooth_2.23-4     lattice_0.19-23
[10] MASS_7.3-12           Matrix_0.999375-50    methylumi_1.8.0
[13] mgcv_1.7-5            nlme_3.1-100          preprocessCore_1.14.0
[16] RSQLite_0.9-4         tools_2.13.0          xtable_1.5-6

_____________________________________________

Naiara G. Bediaga, PhD
Dept of Molecular & Clinical Cancer Medicine
University of Liverpool Cancer Research Centre
200 London Road, Liverpool L3 9TA
United Kingdom

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