BEclear: Batch Effect Detection and Adjustment in DNA Methylation Data.

ABSTRACT: Batch effects describe non-natural variations of, for example, large-scale genomic data sets. If not corrected by suitable numerical algorithms, batch effects may seriously affect the analysis of these datasets. The novel array platform independent software tool BEclear enables researchers to identify those portions of the data that deviate statistically significant from the remaining data and to replace these portions by typical values reconstructed from neighboring data entries based on latent factor models. In contrast to other comparable methods that often use some sort of global normalization of the data, BEclear avoids changing the apparently unaffected parts of the data. We tested the performance of this approach on DNA methylation data for various tumor data sets taken from The Can

SUBMITTER: Akulenko R 

PROVIDER: S-EPMC4999208 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature