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

[Kasper Daniel Hansen]

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
>
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