Hi

Ignore this mail, I found out of it. :-)

Regards,
Ingrid


 
Hi

I have loaded two different files form BeadStudio v3: One with Detection values and one with detection p-values. (A gene with detection 0.7XXX in the first file has a p-value detection of 0.2XXX in the other file)

I use lumiR to read the files: dataSet <- lumiR(dataFil, sep = '\t', detectionTh = 0.5, na.rm = TRUE, lib = NULL)

Then I normalize the data and make an expression matrix: 
dataSet_Norm <- lumiN(dataSet_T, method = c("quantile")) 
dataMatrix <- exprs(dataSet_Norm)

Now I would like to look at which genes that are said to be detected: 
write.table(pData(featureData(dataSet_Norm)), file="Pvalue_detection_v3_mheader.txt")

I make on list of detection values for each data file and the strange is that those two file are identical. Since I use detectionTh = 0.5 the example gene (mentioned at the beginning) should only be said to be detected in the file whit p-values (0.2XXX), or have I misunderstood something?

Regards,
Ingrid

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

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.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"    "0.999375-2"        "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" 




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