[BioC] normalize.quantiles.robust: how to implement weights for different arrays?

[James W. MacDonald]

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


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