Hello everybody, I am using the siggenes package. I have a data set of 45101 genes across 4 experiments. I wanted to perform a two class paired SAM analysis with the data. My data is stored in the form of a 45101*4 matrix(B) and the class vector is like 0,0,1,1B.cl). I have used the following commands to plot my data.. > plot(samtest.out,1.5) where delta value is 1.5. But I cant figure out how to pass the lower and upper horizontal cutoffs to the sam function. So the plot showed all genes marked in green. Can anybody please help me ASAP? Thanks and Regards, Madhurima.

You cannot specify the lower and upper cut off lines. They are specified by the SAM algorithm based on your choice of delta. So if you wanna change the lower and upper cut off lines you have to change delta. See, e.g., http://www.sfb475.uni-dortmund.de/berichte/tr44-03.pdf for an explanation how the lower and upper cutoff are computed for a specified delta. Holger > --- Urspr?ngliche Nachricht --- > Von: madhurima bhattacharjee <madhurima_b at="" persistent.co.in=""> > An: Bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Betreff: [BioC] siggenes package > Datum: Fri, 28 Oct 2005 15:00:03 +0530 > > Hello everybody, > > I am using the siggenes package. > I have a data set of 45101 genes across 4 experiments. > I wanted to perform a two class paired SAM analysis with the data. > My data is stored in the form of a 45101*4 matrix(B) and the class > vector is like 0,0,1,1B.cl). > I have used the following commands to plot my data.. > > > plot(samtest.out,1.5) > where delta value is 1.5. > > But I cant figure out how to pass the lower and upper horizontal cutoffs > to the sam function. > So the plot showed all genes marked in green. > Can anybody please help me ASAP? > > > Thanks and Regards, > Madhurima. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Highspeed-Freiheit. Bei GMX superg?nstig, z.B. GMX DSL_Cityflat,