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@stat.math.ethz.ch"
<bioconductor-request@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@rr-research.no>
> Subject: [BioC] Lumi warning and question
> To: <bioconductor@stat.math.ethz.ch>
> Message-ID:
> <AFE5B2464F1EB547BBACE62CCE8E40200B8118@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 
> 


---------------------------------------------------
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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