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List:       bioconductor
Subject:    Re: [BioC] lumi error?
From:       Pan Du <dupan () northwestern ! edu>
Date:       2007-06-29 14:12:36
Message-ID: C2AA7D85.4131%dupan () northwestern ! edu
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We have added an parameter ³dec² in lumiR function (version 1.3.14). You can
set dec=¹,¹ to solve this problem.

Have a nice day,

Pan


On 6/29/07 8:02 AM, "Ingrid H. G. Østensen"
<Ingrid.H.G.Ostensen@rr-research.no> wrote:

> 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
> 
> 
> 
> 
> 
> 



---------------------------------------------------
Pan Du, PhD
Research Associate / Senior Bioinformatics Analyst
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
676 ST Clair St., #1200
Chicago, IL 60611
Office (312)695-4781
dupan@northwestern.edu
---------------------------------------------------




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