[BioC] Lumi warning and question

[Pan Du]

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 
> 


---------------------------------------------------
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 at northwestern.edu