Consider this study by Michael Mahoney.10 He prepared two papers that were identical in methodology, but different in which theory the
results supported. He sent these papers out for review by reviewers who had earlier expressed support for either the theory supported by the
experimental results, or the theory refuted by the experimental results.
Mahoney found two things: First, reviewers were more likely to reject papers that did not support the theory they favored. This is an expected,
if disappointing, result. Second, he found that reviewers were more critical of the methodology in the papers that did not support their
views---even though the methodologies were identical.
Mahoney, M.J., Publication Prejudices: An experimental study of confirmatory bias in the peer review system. Cognitive Therapy and
Research, 1, 1977, pp. 161--175.