[BioC] vsm2

[Wolfgang Huber]

Dear Richard,

you could do

  library("genefilter")
  rs = rowSds(exprs(richardVSN))

and then do

   hist(rs, col="mistyrose", breaks=100)
   sel = (rs>quantile(rs, 0.9))
   table(sel)


Also, consider using vsn2 rather than vsn.

  Best wishes
	Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


> Dear all,
> I have used vsm2 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)
> 
> matrixForVSM <- 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.U 
> TF-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_ID 
> ENTIFICATION=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"
>