Research
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
Genome Biology 2007, 8:R228 doi:10.1186/gb-2007-8-10-r228
Research
Genome Biology 2007, 8:R228 doi:10.1186/gb-2007-8-10-r228
Data "waves" in SNP array data
Kylie Louise Gorringe (2008-07-01 19:17) Peter MacCallum Cancer Centre
We sometimes observe data "waves" in our Affy SNP array copy number data. It is inconsistent between samples or experimental batches and sometimes a second DNA prep or extra clean-up of the same sample removes the effect. It seems to be more common in whole-genome amplified DNA or DNA from limited sources (eg tumour biopsies). I'd be interested to know if anyone has identified why this occurs or has a solution for analysing tumor data.
Competing interests
None declared
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