[BioC] vsm2

[Richard Harrison]

genius.... i mean vsn...
> Dear all,
> I have used vsn2 on my arrays with an lts.quantile of 0.9. I would  
> like to know how to access the part of the analysis which flags a  
> value as unchanged or changed between the control and test  
> samples ... if there is such a thing.
> Many thanks,
> Richard Harrison
>
>
> Here are the commands i'm using:
>
> my array data is in the ExpressionSet (richard)
>
> matrixForVSN <- exprs(richard)
>
> > dim (matrixForVSN)
> [1] 6553600       2
>
> richardVSN<- vsn(matrixForVSN, lts.quantile=0.9,verbose=T)
>
>
> > sessionInfo()
> R version 2.5.1 (2007-06-27)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB 
> .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. 
> UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 
> ;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "splines"   "grid"      "tools"     "stats"     "graphics"   
> "grDevices"
> [7] "utils"     "datasets"  "methods"   "base"
>
> other attached packages:
> tilingArray       pixmap  geneplotter      lattice     annotate    
> genefilter
>     "1.14.0"      "0.4-7"     "1.14.0"    "0.15-11"      
> "1.14.1"     "1.14.1"
>     survival          vsn        limma  strucchange      
> sandwich          zoo
>       "2.32"      "2.2.0"     "2.10.5"      "1.3-2"       
> "2.0-2"      "1.3-2"
> RColorBrewer         affy       affyio      Biobase
>      "0.2-3"     "1.14.2"      "1.4.1"     "1.14.1"
>
>
>