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k. brand
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@k-brand-1874
Last seen 10.2 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