[BioC] Error in rowname in lumiR?

[Pan Du]

Hi Ingrid,

You need to update the lumi package. This problem should have been solved.
The current version of lumi is 1.0.10.

Version 1.1.0 will be released next week, which will include several new
features, including support of BeadStudio 3.0 format, adding a lumiB
function to allow user adding background correction and a lumiExpresso
function to encapsulate all the preprocessing functions. A QC slot will be
added in the LumiBatch class and the LumiQC class will be removed.

Thanks!


Pan


-------- Original Message --------
Subject: [BioC] Error in rowname in lumiR?
Date: Thu, 22 Mar 2007 09:31:50 +0100
From: Ingrid H. G. Østensen <Ingrid.H.G.Ostensen at rr-research.no>
To: <bioconductor at stat.math.ethz.ch>

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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