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Julian Gehring
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@julian-gehring-5818
Last seen 4.6 years ago

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 n?tiges Paket: Biobase
Lade n?tiges 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 n?tiges Paket: affy
Lade n?tiges Paket: affyio
Lade n?tiges Paket: RColorBrewer
Lade n?tiges Paket: grid
Lade n?tiges Paket: strucchange
Lade n?tiges Paket: zoo
Attache Paket: 'zoo'
The following object(s) are masked from
package:base :
rapply
Lade n?tiges Paket: sandwich
Lade n?tiges Paket: vsn
Lade n?tiges Paket: genefilter
Lade n?tiges Paket: survival
Lade n?tiges Paket: splines
Lade n?tiges Paket: geneplotter
Lade n?tiges Paket: annotate
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Lade n?tiges Paket: pixmap
> library("davidTiling")
Lade n?tiges 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_MONETAR
Y=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"