aCGH / Smooth waves from normalized aCGH data


Smooths the wavy pattern typically seen in aCGH profiles. Note that you need a separate calibration data set, which is not measured from cancer samples. It should be measured with the same array platform and preprocessed with similar normalization settings. When selecting the two input files, be sure to first click on the cancer data set, then on the calibration one. Please note that running this tool can take a couple of hours, depending on the size of the dataset.




aCGH profiles typically show a wavy artifact, which is related to their GC content. Calibration data measured with the same array platform can be used to remove this pattern. It should be normalized with similar settings as the data to smoothed.


Smoothed log ratios of the input file.


Wiel et al. (2009) Smoothing waves in array CGH tumor profiles. Bioinformatics 25: 1099-1104