Dear list, I run CBS to segment 6.0 affy arrays and detect CNVs. I got a plenty of them, and I would like to understand which ones are more likely to be true CN variations and which likely to be noise. Can anybody suggest an approch to do this ? In the DNAcopy package I found the function segments.p >From the help is a little bit hard to understand exaclty if this function is doing this or not. Has anybody looked into it more deeply ? If I try to run the example I get a little odd results with p-values of the order of 10e-296, doe this make sense ? Cheers Marco > set.seed(25) > genomdat <- rnorm(500, sd=0.1) + + rep(c(-0.2,0.1,1,-0.5,0.2,-0.5,0.1,-0.2),c(137,87,17,49,29,52,87,42)) > chrom <- rep(1:2,c(290,210)) > maploc <- c(1:290,1:210) > test1 <- segment(CNA(genomdat, chrom, maploc)) Analyzing: Sample.1 > segments.p(test1) ID chrom loc.start loc.end num.mark seg.mean bstat pval lcl 1 Sample.1 1 1 137 137 -0.2152 24.03078 2.737648e-125 136 2 Sample.1 1 138 224 87 0.1067 34.60294 2.281865e-260 224 3 Sample.1 1 225 241 17 1.0117 49.97221 0.000000e+00 241 4 Sample.1 1 242 290 49 -0.5047 NA NA NA 5 Sample.1 2 1 29 29 0.1917 36.92493 1.416924e-296 29 6 Sample.1 2 30 81 52 -0.4892 36.80884 1.797979e-294 81 7 Sample.1 2 82 168 87 0.0992 15.44993 8.418412e-52 167 8 Sample.1 2 169 210 42 -0.1931 NA NA NA R version 2.7.1 (2008-06-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] DNAcopy_1.14.0 [[alternative HTML version deleted]]