[BioC] Normalization in davidTiling demo

[Julian Gehring]

Hello,

I was trying to run the Segmentation-Demo of the
davidTiling-package. But I always get an error during
normalization:

> xn = normalizeByReference(davidTiling[, isRNA],
davidTiling[, isDNA], pm = PMind, background = isbg)
Fehler in vsn(xn, lts.quantile = 0.95, subsample = 2e+05,
verbose = verbose) : 
        
The likelihood optimization did not converge. A likely
reason is that the normalization parameters are not
uniquely identifiable from the provided data.
Possibly, the columns of the data matrix are exactly
co-linear or affine dependent - please verify the data to
make sure there were no mix-ups.

Well, I don’t assume that the data is co-linear since it
seems to work quite well on other computers.
Does anyone of you have an idea what I could do against
this problem?
Thanks for your help.

Julian Gehring

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

> library("tilingArray")
Lade nötiges Paket: Biobase
Lade nötiges Paket: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For
details
    on reading vignettes, see the openVignette help page.

Lade nötiges Paket: affy
Lade nötiges Paket: affyio
Lade nötiges Paket: RColorBrewer
Lade nötiges Paket: grid
Lade nötiges Paket: strucchange
Lade nötiges Paket: zoo

Attache Paket: 'zoo'


        The following object(s) are masked from
package:base :

         rapply 

Lade nötiges Paket: sandwich
Lade nötiges Paket: vsn
Lade nötiges Paket: genefilter
Lade nötiges Paket: survival
Lade nötiges Paket: splines
Lade nötiges Paket: geneplotter
Lade nötiges Paket: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Lade nötiges Paket: pixmap
> library("davidTiling")
Lade nötiges Paket: GO
> data("davidTiling")
> data("probeAnno")
> nc = as.integer(2560)
> PMind = rep(seq(as.integer(1), nc - as.integer(3), by =
as.integer(2)),
+ each = nc) * nc + (1:nc)
> MMind = PMind + nc
> ispm = rep(FALSE, nc * nc)
> ispm[PMind] = TRUE
> 
> memory.limit(size=4000)
NULL
> isbg = (probeAnno$probeReverse$no_feature == "no" &
probeAnno$probeDirect$no_feature ==
+  "no" & ispm)
> isRNA = davidTiling$nucleicAcid %in% c("poly(A) RNA",
"total RNA")
> isDNA = davidTiling$nucleicAcid %in% "genomic DNA"
> sum(isRNA)
[1] 5
> sum(isDNA)
[1] 3
> xn = normalizeByReference(davidTiling[, isRNA],
davidTiling[, isDNA], pm = PMind, background = isbg)
Fehler in vsn(xn, lts.quantile = 0.95, subsample = 2e+05,
verbose = verbose) : 
        
The likelihood optimization did not converge. A likely
reason is that the normalization parameters are not
uniquely identifiable from the provided data.
Possibly, the columns of the data matrix are exactly
co-linear or affine dependent - please verify the data to
make sure there were no mix-ups.

> sessionInfo()
R version 2.4.1 (2006-12-18) 
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"     

other attached packages:
 davidTiling           GO  tilingArray       pixmap
 geneplotter     annotate 
     "1.0.4"     "1.14.1"     "1.12.0"      "0.4-5"
    "1.12.0"     "1.12.1" 
  genefilter     survival          vsn  strucchange
    sandwich          zoo 
    "1.12.0"       "2.30"     "1.12.0"      "1.3-1"
     "2.0-1"      "1.2-2" 
RColorBrewer         affy       affyio      Biobase 
     "0.2-3"     "1.12.2"      "1.2.0"     "1.12.2"