Hi group, I have a data set of 6 control and 6 disease state(normalised). I want to perform SAM for this to indentify differencially expressed genes with a false discovery rate <15%. I started with the series matrix file by having only the expression values. > source("http://bioconductor.org/biocLite.R") > biocLite("samr") > library("samr") >exprs <- as.matrix(read.table("GSEXXXX_series_matrix_test1_TL.txt",header = TRUE,sep = "\t", row.names = 1, as.is = TRUE)) >samrData<-list(x=exprs,y=rep(1:2,each = 6),geneid = 1:26715,logged2 = TRUE) >samr.obj=samr(samrData, resp.type = "Two class unpaired", testStatistic="standard", nperms=100, random.seed=123456789,s0=0.1) But I am unaware of how to get the list of differencially expressed genes with the following criteria(FDR<15%).Please verify the following steps and help me in writing the code to obtain the final list (passing criteria). Thank u in advance, Viritha [[alternative HTML version deleted]]

Hi group, Let me give more discription of the series matrix file -data contains only expression values and is of 7 columns and 26715 rows including the probe id and the sample names. The session info: R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] samr_1.28 impute_1.24.0 loaded via a namespace (and not attached): [1] tools_2.12.0 Thank u in advance, Viritha On Tue, Nov 16, 2010 at 4:24 PM, viritha kaza <viritha.k@gmail.com> wrote: > Hi group, > I have a data set of 6 control and 6 disease state(normalised). I want to > perform SAM for this to indentify differencially expressed genes with a > false discovery rate <15%. > I started with the series matrix file by having only the expression values. > > > source("http://bioconductor.org/biocLite.R") > > biocLite("samr") > > library("samr") > >exprs <- as.matrix(read.table("GSEXXXX_series_matrix_test1_TL.txt",header > = TRUE,sep = "\t", row.names = 1, as.is = TRUE)) > >samrData<-list(x=exprs,y=rep(1:2,each = 6),geneid = 1:26715,logged2 = > TRUE) > >samr.obj=samr(samrData, resp.type = "Two class unpaired", > testStatistic="standard", nperms=100, random.seed=123456789,s0=0.1) > > But I am unaware of how to get the list of differencially expressed genes > with the following criteria(FDR<15%).Please verify the following steps > and help me in writing the code to obtain the final list (passing criteria). > > Thank u in advance, > Viritha > > [[alternative HTML version deleted]]