```
computeSD.Samples(aCGH.obj, maxChrom = 22, maxmadUse = .3, maxmedUse = .5, maxState = 3, maxStateChange = 100,
minClone = 20)
computeSD.func(statesres, maxmadUse = 0.2, maxmedUse = 0.2, maxState = 3, maxStateChange = 100, minClone = 20, maxChrom = 22)
```

aCGH.obj

Object of class

`aCGH`

.
statesres

The states.hmm object, generally is the output of

`mergeFunc`

.
maxmadUse

Maximum median absolute deviation allowed to
controbute to the overall variability calculation.

maxmedUse

Maximum median value for a state allowed to
contribute to the calculation.

maxState

Maximum number of the states on a given chromosome for
the states from that chromosome to be allowed to enter noise
variability calculation.

maxStateChange

Maximum number of changes from state to state on
a given chromosome for that chromosome to enter noise variability
calculation.

minClone

Minimum number of clones in a state for clones in that
sate to enter variability calculation.

maxChrom

Maxiumum chromosomal index (generally only autosomes
are used for this calculation.

- madChrom
- Returns a matrix containing estimated variability for each chromosome for each sample.
- madGenome
- Returns a vector with estimate of experimental varibility for each sample.

`aCGH`