computeSD.func {aCGH}  R Documentation 
This functions estimate experimental variability of a given sample. This value can be used to rank samples in terms of the quality as well as to derive thresholds for declaring gained and lost clones.
computeSD.Samples(aCGH.obj, maxChrom = 22, maxmadUse = .3, maxmedUse = .5, maxState = 3, minClone = 20) computeSD.func(statesres = states.bic, maxmadUse = 0.2, maxmedUse = 0.2, maxState = 3, maxStateChange = 10, 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. 
Median absolute deviation is estimated in all the states passing the criteria defined by the parameters of the function. Then median of all MADs on individual chromosomes as well as across all chromosomes is taken to estimate chromosomal experimental variability and sample experimental variability.
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. 
Jane Fridlyand
Application of Hidden Markov Models to the analysis of the array CGH data, Fridlyand et.al., JMVA, 2004