[R] a question about "sign" of "cgh" package

XinMeng xmeng at capitalbio.com
Mon Mar 26 08:43:24 CEST 2007


Hi all :
I'm a user of "cgh" package. Here's a question about "sign".
  
As to help on "sign":
sign = +1 is used to detect polysomy (regions of copy number change increase) in test:control logratios.
 
sign = -1 is used ¨C inverting the sign of the logratios ¨C to detect deletions (regions of copy number decrease).
 
I wanna know whether my opinion about "sign" is correct:
If I think ratio > 2 and ratio < 0.5 are considered as copy number increase and decrease respectively.
So the corresponding sign is log2(2):+1 and log2(0.5):-1 respectively.
 
If I think ratio > 1.5 and ratio < 0.67 are considered as copy number increase and decrease respectively.
So the corresponding sign is log2(1.5):+0.585  and log2(1/1.5):-0.585 respectively.
 
I wanna know whether I'm right on "sign".
 
If not ,how can I use "sign" according to different "ratio" threshold of copy number increase and decrease?
 
Thanks a lot for your help!
 
My best regards



More information about the R-help mailing list