Many and various influences can bias research; funding is only one of these. Funding agencies -- both private and public -- should not have specific expectations for the research they fund other than a commitment to the scientific method and the successful completion of a proposed project. If an agency has specific expectations for the results, I would avoid seeking their funds. This is a complex problem given the limited availability of research dollars. Consequently, one of the goals in my lab is to establish a portfolio of diversified funding.

Howard has given a very thoughtful response. Most funders of scientific research want to test and increase knowledge of a topic and so are less interested in outcomes than in methods. However, commercial funders can have vested interests, for example, in seeing their product's performance relative to competing brands. In these cases, I suggest consulting your research office to ensure the funding agreement you have gives you complete independence in the research design, data analysis and interpretation, and publication of the findings.