Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)

Abstract Background An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error. Results We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries") and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it. Conclusion Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site.

Optical aids for low vision: use of the Internet to guide teachers of the visually impaired

PURPOSES: To describe and interpret teachers' opinions about and responsiveness to guidance on optical aids for low vision. METHODS: It was conducted a cross-sectional analytical study. The convenience, non-random sample consisted of 58 teachers from the public school network of the city of Campinas. It was constructed and applied a structured questionnaire, available online at the assessed website. For qualitative data collection it was conducted an exploratory study using the focus group technique. RESULTS: Responses expressed, for the most part, a marked interest in the website, its easiness of access, and the comprehensive nature of the information provided. Most people reported frequent use of the Internet to seek information, and found it easier to access the Internet at home. Among the qualitative aspects of the evaluation, we should mention the perceived importance of the website as a source of information, despite some criticism about the accessibility and reliability of the information found on the Internet. CONCLUSION: Teachers' need for training to deal with visually impaired students and their positive response to advice and information lead to the conclusion that web-based guidelines on the use of optical aids were considered beneficial to ease the understanding of visual impairment and the rehabilitation of the affected subjects.