Hi,
I would like some extra information on the 'cgh' package in R. I noticed
that there isn't much activity regarding this package on the R and BioC
mailing list (I googled it).
I started using this package and I have few questions:
1/ As I have a custom tiling like array @8um features resolution (affy),
I have a lot of probes to work with. I'm assuming it is correct to split
my data by chromosomes (I work on Plasmodium): 14 chromosomes, no sexual
chromosome, so nothing really expected in terms of polysomy.
2/ For each chromosome, I'm computing the robustness, the threshold, the
sw and the sw.perm.test before to plot with sign=-1 and a second plot
sign=+1
- Do I need to change the threshold's sign when I plot? (if
the threshold is -1, I plot sign=-1, but if I do sign=+1 with the same
threshold -1, how wrong is that?)
- How do you export the high scoring islands? If I inspect the
sw object created by sw(), the highest score doesn't seem to correspond
to the blue line generated by the sw.plot as "highest scoring island".
- In the sw object, are the values of score, start, length,
sorted for the highest score? They seem to be... but I couldn't find any
documentation about it
- Is the sw.perm also sorted for the highest score? Or is it
for the highest p value?
What I really want is to be able to write.table() for the islands
location, and the best score, ideally, the ones corresponding to the
island(s) plotted by the sw.plot().
Here is the exemple code of what I used:
x <- sw.threshold(intens[,8], function(x) median(x) + .2 * mad(x), -1)
r <- sw.rob(intens[,8])
sw <- sw(x,max.nIslands = NULL, trace = F)
sw.perm <- sw.perm.test(x, max.nIslands = NULL, nIter= 1e4)
sw.plot(intens[,8], location = coords[,2],threshold.func = function(x)
median(x) + .2 * mad(x), sign = -1, expected = NULL, legend =
TRUE,rob=r,main=paste("chrom 9 loss p=",sw.perm[1]))
sessionInfo()
R version 2.6.0 (2007-10-03)
ia64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cgh_1.0-2
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Thank you very much for your help,
Best wishes
celine
**************************************
Celine Carret, PhD
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton, Cambridge
CB10 1SA, UK
tel.+44-1223494940
fax.+44-1223494919
**************************************
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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