Table 2

Computational performance
Method R package Agilent 244K Illumina 1.1M
Raw data Outliers removed Raw data Outliers removed
PCF copynumber 4 (0.2) 4 (0.2) 23 (0.7) 22 (0.4)
Fused Lasso cghFLasso 5 (0.2) 5 (0.2) 97 (0.7) 99 (3.3)
CBS DNAcopy 15 (4.7) 35 (4.1) 71 (12.9) 219 (12.8)

The average computation time (in seconds) per sample is shown for copynumber (PCF), DNAcopy v1.30.0 (CBS) and cghFLasso v0.2-1 (Fused Lasso) on the MicMa 244 K data set (49 samples) and on the logR values from an Illumina 1.1 M SNP array data set (6 samples). The IQR over samples is given in parenthesis. The methods were applied to both raw data and data with outliers removed using the Winsorization method. All tests were performed on a PC with a 2.93GHz Intel i7 CPU with 8 Gb of memory running Windows 7 and R 2.15.1 (64-bit).

Nilsen et al.

Nilsen et al. BMC Genomics 2012 13:591   doi:10.1186/1471-2164-13-591

Open Data