Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis.

ABSTRACT:

Background

DNA methylation microarrays have become an increasingly popular means of studying the role of epigenetics in cancer, although the methods used to analyze these arrays are still being developed and existing methods are not always widely disseminated among microarray users.

Methods

We investigated two problems likely to confront DNA methylation microarray users: (i) batch effects and (ii) the use of widely available pathway analysis software to analyze results. First, DNA taken from individuals exposed to low and high levels of drinking water arsenic were plated twice on Illumina's Infinium 450 K HumanMethylation Array, once in order of exposure and again following randomization. Second, we conducted simulations in which random CpG sites were drawn from the 450 K ar

SUBMITTER: Harper KN 

PROVIDER: S-EPMC3687782 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature