[BioC] vsm2

Richard Harrison harryinashed at mac.com
Fri Sep 28 16:43:27 CEST 2007


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"



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