Hi

I have found out what was wrong. Some time in the past 3 weeks my version of BeadStudio found out that it would like to be Norwegian (without telling me) In other words: In the header of the data file Local Settings = nb-NO and the decimal separator is no longer (.) but (,). When I replaced all (,) with (.) it worked fine, even the file from version 3 of BeadStudio. 

Maybe you should some where mention that using (,) is not a good idea, or make the lumi package write out an error message that is understandable. :-)

Regards,
Ingrid



Hi Ingrid,

Please try the latest version of lumi (version 1.3.13), which can be
downloaded from Bioconductor developing website:
http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html
Tell me if the problem still exists.
Thanks!


Pan


Message: 17
Date: Thu, 28 Jun 2007 10:47:46 +0200
From: Ingrid H. G. ?stensen     <Ingrid.H.G.Ostensen@rr-research.no>
Subject: [BioC] lumi error?
To: <bioconductor@stat.math.ethz.ch>
Message-ID:
    <AFE5B2464F1EB547BBACE62CCE8E40200B8102@mr3k6001.ad.medicalresearch.no>
    
Content-Type: text/plain

Hi 

I am using the lumi package to analyze our Illumina data and I have used
human version 2 and BeadStudio version 2 to extract data to use in
R/Bioconductor. This has worked fine. But now I have used human version 1
and BeadStudio version 3 and I get the following error message when I try to
read the data into R:

> dataSet <- lumiR(dataFil)
Error in var(x, na.rm = na.rm) : 'x' is empty
In addition: Warning messages:
1: NAs introduced by coercion
2: NAs introduced by coercion
3: NAs introduced by coercion
4: no non-missing arguments to max; returning -Inf

> sessionInfo()
R version 2.5.0 (2007-04-23)
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"
[9] "base"     

other attached packages:
        annaffy         GOstats        Category          Matrix
lattice      genefilter
        "1.8.1"         "2.2.1"         "2.2.2"     "0.99875-2"
"0.15-11"        "1.14.1"
       survival            KEGG            RBGL              GO
graph illuminaHumanv1
         "2.32"        "1.16.0"        "1.12.0"        "1.16.0"
"1.14.2"         "1.2.0"
         xtable    RColorBrewer           limma            lumi
annotate            mgcv
        "1.4-6"         "0.2-3"        "2.10.0"         "1.2.0"
"1.14.1"        "1.3-25"
           affy          affyio         Biobase
       "1.14.0"         "1.4.0"        "1.14.0"

Does anyone have any idea what might be wrong?

Regards,
Ingrid






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