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_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] DNAcopy_1.14.0

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