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.UT F- 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"

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" > > >

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;L C_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" >