<filename>text/zotero/11/tiling-array-analysis.bib
@article{karpikov_tiling_2011,
	title = {Tiling array data analysis: a multiscale approach using wavelets},
	volume = {12},
	issn = {1471-2105},
	url = {http://www.biomedcentral.com/1471-2105/12/57},
	doi = {10.1186/1471-2105-12-57},
	shorttitle = {Tiling array data analysis},
	abstract = {Abstract: "{BACKGROUND}: Tiling array data is hard to interpret due to noise. The wavelet transformation is a widely used technique in signal processing for elucidating the true signal from noisy data. Consequently, we attempted to denoise representative tiling array datasets for {ChIP}-chip experiments using wavelets. In doing this, we used specific wavelet basis functions, Coiflets, since their triangular shape closely resembles the expected profiles of true {ChIP}-chip peaks. {RESULTS}: In our wavelet-transformed data, we observed that noise tends to be confined to small scales while the useful signal-of-interest spans multiple large scales. We were also able to show that wavelet coefficients due to non-specific cross-hybridization follow a log-normal distribution, and we used this fact in developing a thresholding procedure. In particular, wavelets allow one to set an unambiguous, absolute threshold, which has been hard to define in {ChIP}-chip experiments. One can set this threshold by requiring a similar confidence level at different length-scales of the transformed signal. We applied our algorithm to a number of representative {ChIP}-chip data sets, including those of Pol {II} and histone modifications, which have a diverse distribution of length-scales of biochemical activity, including some broad peaks. {CONCLUSIONS}: Finally, we benchmarked our method in comparison to other approaches for scoring {ChIP}-chip data using spike-ins on the {ENCODE} Nimblegen tiling array. This comparison demonstrated excellent performance, with wavelets getting the best overall score."},
	pages = {57},
	number = {1},
	journaltitle = {{BMC} Bioinformatics},
	author = {Karpikov, <NAME> Rozowsky, <NAME> Gerstein, Mark},
	urldate = {2011-02-22},
	date = {2011}
}

