[BioC] Lumi warning and question
James W. MacDonald
jmacdon at med.umich.edu
Mon Aug 27 17:38:47 CEST 2007
Hi Ingrid,
The problem here is you are using the devel version of lumi on a release
version of R/BioC. If you want to use the devel version(s), you need to
start with R-2.6.0devel and then install lumi using biocLite().
Best,
Jim
Ingrid H. G. Østensen wrote:
> Hi
>
> I got that part. :-)
>
> But how do I get the package? I tried the following:
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("AnnotationDbi")
> Running biocinstall version 2.0.8 with R version 2.5.1
> Your version of R requires version 2.0 of Bioconductor.
> Warning message:
> package 'AnnotationDbi' is not available
>
> And I can not find int the BioC Release Packages (or am I blind at the moment?)
>
> Regards,
> Ingrid
>
> You need to install ³AnnotationDbi² package, which is related with
> ³annotate² package for the Bioconductor 2.1. Maybe you also need to install
> some other packages related with the Bioconductor 2.1 update. Please check
> the error message to see which package may be needed.
>
> Pan
>
>
> On 8/27/07 9:00 AM, "Ingrid H. G. Østensen"
> <Ingrid.H.G.Ostensen at rr-research.no> wrote:
>
>> Hi
>>
>> I installed the new version and now I got error messages when I loaded the
>> libraries:
>>
>>>> library(lumi)
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> Welcome to Bioconductor
>>
>> Vignettes contain introductory material. To view, type
>> 'openVignette()'. To cite Bioconductor, see
>> 'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: affy
>> Loading required package: affyio
>> Loading required package: mgcv
>> This is mgcv 1.3-26
>> Loading required package: annotate
>> Error in loadNamespace(name) : there is no package called 'AnnotationDbi'
>> In addition: Warning message:
>> package 'lumi' was built under R version 2.6.0
>> Error in as.environment(pos) : no item called "newtable" on the search list
>>>> library(limma)
>>>> library(RColorBrewer)
>>>> library(xtable)
>>>> library(annotate)
>>>> library(annaffy)
>> Loading required package: GO
>> Loading required package: KEGG
>>>> library(GOstats)
>> Loading required package: graph
>> Loading required package: RBGL
>> Loading required package: Category
>> Loading required package: genefilter
>> Loading required package: survival
>> Loading required package: splines
>> Loading required package: Matrix
>> Loading required package: lattice
>>>> library(illuminaHumanv2)
>>>>
>>>> sessionInfo()
>> R version 2.5.1 (2007-06-27)
>> 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" "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 annotate mgcv affy
>> "1.8.1" "1.16.1" "1.16.0" "1.5-1"
>> "1.0-1" "2.10.5" "1.14.1" "1.3-26" "1.14.2"
>> affyio Biobase
>> "1.4.1" "1.14.1"
>> Regards,
>> Ingrid
>>
>>
>>
>> Hi Ingrid,
>>
>> I found you were still using the old lumi version 1.2.0. Due to the actively
>> developing of lumi package, the latest version is 1.3.26. So please try the
>> new version first and tell me this problem still exists. Thanks!
>>
>> Please check this link:
>> http://www.bioconductor.org/packages/2.1/bioc/html/lumi.html
>>
>>
>> Pan
>>
>>
>> On 8/27/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
>> <bioconductor-request at stat.math.ethz.ch> wrote:
>>
>>>> Message: 3
>>>> Date: Mon, 27 Aug 2007 09:45:06 +0200
>>>> From: Ingrid H. G. ?stensen <Ingrid.H.G.Ostensen at rr-research.no>
>>>> Subject: [BioC] Lumi warning and question
>>>> To: <bioconductor at stat.math.ethz.ch>
>>>> Message-ID:
>>>> <AFE5B2464F1EB547BBACE62CCE8E40200B8118 at mr3k6001.ad.medicalresearch.no>
>>>>
>>>> Content-Type: text/plain
>>>>
>>>> Hi
>>>>
>>>> I have been using the lumi package for a while and I am currently using it
>>> on
>>>> 6 arrays (2 groups). I have gotten two warnings, that I have not seen
>>> before:
>>>> dataSet <- lumiR(dataFil)
>>>> Warning message:
>>>> NAs introduced by coercion in: as.double.default(exprs)
>>>>
>>>>
>>>> jpeg(file = VST_plott,pointsize = 12, width = 650, height = 730)
>>>> plotVST(dataSet_T, main = "Data transformation")
>>>> Warning message:
>>>> NaNs produced in: log(x)
>>>> dev.off()
>>>>
>>>> I am also wondering about the number of "interestin" genes that are growing
>>>> after the background adjustment, transformation and normalization. Compare
>>> the
>>>> headings in figure 8 and 16 in the lumi vignette and you can see what I am
>>>> wondering about.
>>>>
>>>>>> sessionInfo()
>>>> R version 2.5.1 (2007-06-27)
>>>> 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" "base"
>>>>
>>>> other attached packages:
>>>> illuminaHumanv2 GOstats Category Matrix
>>>> lattice genefilter survival RBGL graph
>>>> "1.2.0" "2.2.6" "2.2.3" "0.999375-1"
>>>> "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"
>>>>
>>>>
>>>> Regards,
>>>> Ingrid
>>>>
>>
>
>
>
>
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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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