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 [[alternative HTML version deleted]]