Normalization in Chr X and Y

[Viggy0205]

Can you please let me know how the normalization happens in specific to sex chromosomes and if it is any different from the autosomal chromosomes?

Also, why are you taking a factor of 2 in line 101 in the R script cnSegments.R?

[chrisamiller]

  ##convert means back out of log space into absolute copy number
  segs$seg.mean=(2^segs$seg.mean)*2

to convert from log2 copy number to absolute (2 = cn neutral, 1 = loss, etc), that's the formula

The normalization for GC content and mapability is applied to both autosomes and sex chromosomes in the same manner

[Viggy0205]

I have two more questions and it would be great if you could answer them as well:

1. The output that I got for the copycat was in the log values (decimal) and not absolute values in the 5th column of the "alts.paired.dat or segs.paired.dat" file
2. In the 5 column output file "alts.paired.dat or segs.paired.dat", what is the 4th column for? When I checked the R script used, I found it stands for #probes. So what exactly is meant by probes in the CNV context?

[chrisamiller]

1. the output is expressed in terms of copy number, where 2 equals CN neutral. There may be many factors that cause the CN to be something other than integer values (tumor purity, subclonal events, or just plain noise)

2. The 4th column is the number of consecutive windows included in the segment