[BioC] Normalization in davidTiling demo

[Julian Gehring]

Hi Wolfgang,

I upgraded to tilingArray 1.13.3 and R-2.5 and I also
upgraded all the other packages as far as I could, but I'm
afraid with no effect.
The problem doesn't occur on Linux, everything works fine
there.
Thanks for your quick response and help.

Greetings
Julian Gehring

-------
> sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-26
r40806) 
i386-pc-mingw32 

locale:
LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252

attached base packages:
 [1] "splines"   "grid"      "tools"     "stats"
    "graphics"  "grDevices"
 [7] "utils"     "datasets"  "methods"   "base"     

davidTiling        GO     tilingArray   pixmap  geneplotter
   annotate 
     "1.0.4"   "1.15.1"     "1.13.3"    "0.4-6"
    "1.12.0"   "1.13.6"
  genefilter    survival        vsn  strucchange   sandwich
   zoo 
    "1.13.8"      "2.31"   "2.0.15"      "1.3-1"    "2.0-1"
   "1.2-2"
RColorBrewer         affy       affyio      Biobase 
     "0.2-3"    "1.13.14"      "1.3.3"    "1.13.39"





-----Original Message-----
From: Wolfgang Huber [mailto:huber at ebi.ac.uk] 
Sent: Mittwoch, 28. Februar 2007 18:12
To: Julian Gehring
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Normalization in davidTiling demo

Hi Julian,

I have heard about this problem now a few times from people
that use R
2.4 and Bioconductor release 1.9 on Windows, but was never
able to
reproduce it. I have just rerun the vignettes
"segmentation.Rnw" and
"assessNorm.Rnw" from the tilingArray/inst/scripts
directory on the
system detailed below(*), with no problems. (Note that you
don't need to
type the commands from the PDF, but can use the functions
'Sweave' or
'Stangle' to process vignettes.)

So, to nail this down:

1. Does your problem persist if you upgrade to tilingArray
version
1.13.3?
http://bioconductor.org/packages/2.0/bioc/html/tilingArray.html
Since the version you used, there have been a number of
updates in
particular to the normalizeByReference function.

2. If yes, does it persist if you use the R devel (to be
2.5) snapshot
build: http://www.stats.bris.ac.uk/R/bin/windows/base

3. If yes, does it also occur on Linux or Mac?

Once we have the answer to these, we can see further.
Thanks for pointing this out and helping to trace it down.

 Best wishes
  Wolfgang Huber
  EBI



(*) > sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-28
r40808)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] "splines"   "grid"      "tools"     "stats"
    "graphics"  "grDevices"
 [7] "utils"     "datasets"  "methods"   "base"

other attached packages:
Scerevisiaetilingprobe            matchprobes
           davidTiling
               "1.1.0"                "1.7.4"
               "1.2.1"
                    GO            tilingArray
                pixmap
              "1.15.1"               "1.13.3"
               "0.4-6"
           geneplotter                lattice
              annotate
              "1.13.7"              "0.14-16"
              "1.13.6"
            genefilter               survival
                   vsn
              "1.13.8"                 "2.31"
              "2.0.16"
           strucchange               sandwich
                   zoo
               "1.3-1"                "2.0-1"
               "1.2-2"
          RColorBrewer                   affy
                affyio
               "0.2-3"              "1.13.14"
               "1.3.3"
               Biobase               fortunes
             "1.13.39"                "1.3-2"