Quantile smoothing of array CGH data.
BACKGROUND
Plots of array Comparative Genomic Hybridization (CGH) data often show special patterns: stretches of constant level (copy number) with sharp jumps between them. There can also be much noise. Classic smoothing algorithms do not work well, because they introduce too much rounding. To remedy this, we introduce a fast and effective smoothing algorithm based on penalized quantile regression. It can compute arbitrary quantile curves, but we concentrate on the median to show the trend and the lower and upper quartile curves showing the spread of the data. Two-fold cross-validation is used for optimizing the weight of the penalties.


RESULTS
Simulated data and a published dataset are used to show the capabilities of the method to detect the segments of changed copy numbers in array CGH data.
Eilers
Paul H C
PH
Department of Medical Statistics, Leiden University Medical Centre PO Box 9604, 2300 RC, Leiden, The Netherlands. p.eilers@lumc.nl
de Menezes
Renée X
RX
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D017403:In Situ Hybridization / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity