Dear
When I run PSCBS segmentation and LOH calling, there was an error. Part of
error message is shown below. I do not know which sample caused this error,
which was bad. It had run for several days. Do you know what is wrong ? Do
you think the sample we (Henrik) discussed before caused this
(https://groups.google.com/forum/#!topic/aroma-affymetrix/FGu8J_44Wkg)?
Segment #840 of 840...done
ROH calls:
logi [1:840] FALSE NA FALSE NA FALSE FALSE ...
Mode FALSE TRUE NA's
logical 623 72 145
Calling ROH...done
Calling segments of allelic balance from one-sided DH bootstrap confidence
intervals...
delta (offset adjusting for bias in DH): 0.122733550840777
alpha (CI quantile; significance level): 0.05
Calling segments...
Number of segments called allelic balance (AB): 495 (58.93%) of 840
Calling segments...done
Calling segments of allelic balance from one-sided DH bootstrap confidence
intervals...done
[2015-03-04 23:14:46] Exception: Argument 'delta' is out of range [0,Inf]:
-0.67309916
at #14. getNumerics.Arguments(static, ..., asMode = "double", disallow =
disallow)
- getNumerics.Arguments() is in environment 'R.utils'
at #13. getNumerics(static, ..., asMode = "double", disallow = disallow)
- getNumerics() is in environment 'R.utils'
at #12. getDoubles.Arguments(static, ..., length = length)
- getDoubles.Arguments() is in environment 'R.utils'
at #11. getDoubles(static, ..., length = length)
- getDoubles() is in environment 'R.utils'
at #10. getDouble.Arguments(static, ...)
- getDouble.Arguments() is in environment 'R.utils'
at #09. getDouble(static, ...)
- getDouble() is in environment 'R.utils'
- originating from '<text>'
at #08. Arguments$getDouble(delta, range = c(0, Inf))
- Arguments$getDouble() is local of the calling function
at #07. callLowC1ByC1.PairedPSCBS(fit, ..., callName = "loh")
- callLowC1ByC1.PairedPSCBS() is in environment 'PSCBS'
at #06. callLowC1ByC1(fit, ..., callName = "loh")
- callLowC1ByC1() is in environment 'PSCBS'
at #05. callLOH.PairedPSCBS(fit, delta = deltaLOH)
- callLOH.PairedPSCBS() is in environment 'PSCBS'
at #04. callLOH(fit, delta = deltaLOH)
- callLOH() is in environment 'PSCBS'
- originating from '/homes/cliu/czliu/czliu/azhar/function.R'
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