Hi

I posted a message yesterday regarding the lumi package. I have been looking at the code for the lumiR procedure and found the line were things are going wrong:

rownames(allData) <- targetID 

The error message that comes is: 

Error in `row.names<-.data.frame`(`*tmp*`, value = c("ILMN_10000", "ILMN_100000",  :         duplicate 'row.names' are not allowed

Is seems that rownames can not see the difference between the different Illumina target ID’s, example of ID:

ILMN_10000
ILMN_100000
ILMN_100007
ILMN_100009
ILMN_10001
ILMN_100010
ILMN_10002
ILMN_100028
ILMN_100030
ILMN_100031
ILMN_100034
ILMN_100037
ILMN_10004
ILMN_10005
ILMN_100054
ILMN_100059
ILMN_10006
ILMN_100075
ILMN_100079
ILMN_100083
ILMN_100084
ILMN_100086
ILMN_10009
ILMN_100091
ILMN_100097
ILMN_1001
ILMN_10010
ILMN_100101
ILMN_100106
ILMN_10011
ILMN_100114
ILMN_10012
 

More information:

class(allData)
[1] "data.frame"

class(targetID)
[1] "character"

sessionInfo()
R version 2.4.1 (2006-12-18) 
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] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"   "base"     

other attached packages:
      xtable RColorBrewer        limma         lumi         mgcv         affy       affyio      Biobase 
     "1.4-3"      "0.2-3"     "2.9.13"      "1.0.3"     "1.3-23"     "1.12.2"      "1.2.0"     "1.12.2" 

Does anyone have any suggestions about what might be wrong, can it be because I use R 2.4.1 and the package is for R 2.5.x? Or can it be something with the data file that contains the Illumina data.


Regards,
Ingrid


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