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

**************************************






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