Question: Normalization in davidTiling demo
0
gravatar for Julian Gehring
12.7 years ago by
Julian Gehring1.3k
Julian Gehring1.3k wrote:
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"
ADD COMMENTlink modified 12.7 years ago by Wolfgang Huber13k • written 12.7 years ago by Julian Gehring1.3k
Answer: Normalization in davidTiling demo
0
gravatar for Wolfgang Huber
12.7 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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 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_MONET ARY=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"
ADD COMMENTlink written 12.7 years ago by Wolfgang Huber13k
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