[BioC] snapCGH: log2ratio

[Sean Davis]

caiwei at mdanderson.org wrote:
> John,
>
> Thanks,
>
> What does this command do (in the user guide)? does it affect Log2Ratio?
>
> RG$design<-c(-1,-1)
>   

A quick glance at the code for log2ratios() reveals that the design 
component of either the MAList or SegList is not accessed when returning 
the results, so it does not correct for dye swaps.  However, if one 
looks at the code for the run...() functions, the first few lines DO use 
the $design component, so any calculations done for the segmentation do 
correct for dye swaps.  It is probably worth a quick glance at the code 
to satisfy yourself that you know what is going on.  You can see code by 
typing the function without any arguments or parentheses:

log2ratios
runDNAcopy

etc.

Hope that helps,
Sean