[BioC] Normalization in davidTiling demo
Wolfgang Huber
huber at ebi.ac.uk
Wed Feb 28 18:11:30 CET 2007
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"
> 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"
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