[BioC] CGH analysis warning messages

[Ian Roberts]

Daniel Brewer <daniel.brewer at ...> writes:

> 
> After running processCGH() I get the following:
> collapsing to unique 'x' values in: approx(lowess(kbl[ind], vecl[ind], f
> = smooth), xout = kbl[-ind])

Dan,
  Don't know the answer - just a possible stab in the dark.  Errors in 
processCGH like the ones you are getting might be caused by too few 
observations (too many NAs) in the MA data.  You could try either (1) impute 
missing values, or (2) cut down on the number of autosomes you process to see 
if one particular chromosome is misbehaving.  I get a similar error in aCGH 
package if I include Chr 22 in my analysis - not enough data points.

> 
> And after running runDNAcopy() I get:
> Warning message:
> array has repeated maploc positions

I get the exact same error ... re:DNAcopy, but BioHMM and GLAD all work fine 
let me know if you uncover the answer.
Best wishes,

Ian