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

k. brand k.brand at erasmusmc.nl
Mon Sep 18 20:09:28 CEST 2006


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



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