Hi

I have been using the lumi package for a while and I am currently using it on 6 arrays (2 groups). I have gotten two warnings, that I have not seen before: 

dataSet <- lumiR(dataFil)
Warning message:
NAs introduced by coercion in: as.double.default(exprs) 


jpeg(file = VST_plott,pointsize = 12, width = 650, height = 730)                                
plotVST(dataSet_T, main = "Data transformation")
Warning message:
NaNs produced in: log(x) 
dev.off() 

I am also wondering about the number of "interestin" genes that are growing after the background adjustment, transformation and normalization. Compare the headings in figure 8 and 16 in the lumi vignette and you can see what I am wondering about. 

> sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian (Bokmål)_Norway.1252;LC_MONETARY=Norwegian (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     

other attached packages:
illuminaHumanv2         GOstats        Category          Matrix         lattice      genefilter        survival            RBGL           graph 
        "1.2.0"         "2.2.6"         "2.2.3"    "0.999375-1"        "0.16-3"        "1.14.1"          "2.32"        "1.12.0"        "1.14.2" 
        annaffy            KEGG              GO          xtable    RColorBrewer           limma            lumi        annotate            mgcv 
        "1.8.1"        "1.16.1"        "1.16.0"         "1.5-1"         "1.0-1"        "2.10.5"         "1.2.0"        "1.14.1"        "1.3-26" 
           affy          affyio         Biobase 
       "1.14.2"         "1.4.1"        "1.14.1" 


Regards,
Ingrid 



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