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
>
>

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