normalize.quantiles.robust: how to implement weights for different arrays?
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k. brand ▴ 420
@k-brand-1874
Last seen 8.3 years ago
Dear BioCers, Regarding- normalize.quantiles.robust(x,weights=NULL, Can some one illustrate how to implement weights for my different arrays? Im trying to 'up weight' a good hyb against a not so good hyb, in an otherwise standard RMA approach. Trying to follow the package description i failed to effect this (see failed attempt below). Any suggestions greatly appreciated. thanks in advance, Karl > library(affyPLM) Loading required package: affydata Loading required package: gcrma Loading required package: matchprobes > dat <- ReadAffy() > datbg <- bg.correct.rma(dat) >normalize.quantiles.robust(datbg,weights="Tco1A.CEL"=1,"Tmi1A.CEL"=1 ,"Tsh1A.CEL"=1,"Tco2A.CEL"=1, Error: syntax error in normalize.quantiles.robust(datbg,weights="Tco1A.CEL"=" > "Tmi2A.CEL"=1,"Tsh2A.CEL"=1,"Tco3B.CEL"=2,"Tmi3B.CEL"=2, Error: syntax error in ""Tmi2A.CEL"=1," > "Tsh3B.CEL"=2,"Tco4B.CEL"=2,"Tmi4B.CEL"=2,"Tsh4B.CEL"=2) Error: syntax error in ""Tsh3B.CEL"=2," > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: mouse4302cdf affyPLM gcrma matchprobes affydata affy "1.12.0" "1.8.0" "2.4.1" "1.4.0" "1.8.0" "1.10.0" affyio Biobase "1.0.0" "1.10.0" -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Cell Biology and Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam lab +31 (0)10 408 7409 fax +31 (0)10 408 9468
cdf gcrma matchprobes affyPLM affyio cdf gcrma matchprobes affyPLM affyio • 660 views
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@kasper-daniel-hansen-2979
Last seen 10 weeks ago
United States
I have not tried using the weight argument myself, but looking at your code it is obvious that you are missing a c() around the argument: you need to make it a vector, like normalize...(databg, weights = c(1,2,3,...)) From reading the help page and looking at the R code it is unclear to me whether there is any name matching going on, so I would assume you need to make sure your vector of weights have the same order as the chips in the databg object. Kasper On Sep 18, 2006, at 11:09 AM, k. brand wrote: > Dear BioCers, > > Regarding- > > normalize.quantiles.robust(x,weights=NULL, > > Can some one illustrate how to implement weights for my different > arrays? > > Im trying to 'up weight' a good hyb against a not so good hyb, in an > otherwise standard RMA approach. Trying to follow the package > description i failed to effect this (see failed attempt below). Any > suggestions greatly appreciated. > > thanks in advance, > > Karl > > >> library(affyPLM) > Loading required package: affydata > Loading required package: gcrma > Loading required package: matchprobes >> dat <- ReadAffy() >> datbg <- bg.correct.rma(dat) >> normalize.quantiles.robust >> (datbg,weights="Tco1A.CEL"=1,"Tmi1A.CEL"=1,"Tsh1A.CEL"=1,"Tco2A.CEL"= >> 1, > Error: syntax error in > normalize.quantiles.robust(datbg,weights="Tco1A.CEL"=" >> "Tmi2A.CEL"=1,"Tsh2A.CEL"=1,"Tco3B.CEL"=2,"Tmi3B.CEL"=2, > Error: syntax error in ""Tmi2A.CEL"=1," >> "Tsh3B.CEL"=2,"Tco4B.CEL"=2,"Tmi4B.CEL"=2,"Tsh4B.CEL"=2) > Error: syntax error in ""Tsh3B.CEL"=2," > > >> sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" > "utils" > [7] "datasets" "base" > > other attached packages: > mouse4302cdf affyPLM gcrma matchprobes affydata > affy > "1.12.0" "1.8.0" "2.4.1" "1.4.0" "1.8.0" > "1.10.0" > affyio Biobase > "1.0.0" "1.10.0" > > > -- > Karl Brand <k.brand at="" erasmusmc.nl=""> > Department of Cell Biology and Genetics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > lab +31 (0)10 408 7409 fax +31 (0)10 408 9468 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
k. brand wrote: > Dear BioCers, > > Regarding- > > normalize.quantiles.robust(x,weights=NULL, > > Can some one illustrate how to implement weights for my different arrays? > > Im trying to 'up weight' a good hyb against a not so good hyb, in an > otherwise standard RMA approach. Trying to follow the package > description i failed to effect this (see failed attempt below). Any > suggestions greatly appreciated. > > thanks in advance, > > Karl > > > > library(affyPLM) > Loading required package: affydata > Loading required package: gcrma > Loading required package: matchprobes > > dat <- ReadAffy() > > datbg <- bg.correct.rma(dat) > >normalize.quantiles.robust(datbg,weights="Tco1A.CEL"=1,"Tmi1A.CEL" =1,"Tsh1A.CEL"=1,"Tco2A.CEL"=1, From the help for normalize.quantiles.robust() weights: A vector of weights, one for each chip What you have passed is not a vector of weights. As far as R is concerned, you have passed a character string "Tco1A.CEL", followed by a bunch of other arguments that don't match up to the available arguments in the function call. You need something like weights = rep(1:2, each = 6) Which will be a vector of weights. You might consider perusing "An Introduction to R". Best, Jim > Error: syntax error in > normalize.quantiles.robust(datbg,weights="Tco1A.CEL"=" > > "Tmi2A.CEL"=1,"Tsh2A.CEL"=1,"Tco3B.CEL"=2,"Tmi3B.CEL"=2, > Error: syntax error in ""Tmi2A.CEL"=1," > > "Tsh3B.CEL"=2,"Tco4B.CEL"=2,"Tmi4B.CEL"=2,"Tsh4B.CEL"=2) > Error: syntax error in ""Tsh3B.CEL"=2," > > > > sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "base" > > other attached packages: > mouse4302cdf affyPLM gcrma matchprobes affydata > affy > "1.12.0" "1.8.0" "2.4.1" "1.4.0" "1.8.0" > "1.10.0" > affyio Biobase > "1.0.0" "1.10.0" > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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