Archive for the ‘trainee author’ Category

Significance v. fold change

28 January 2010 Leave a comment

C. M. Yanofsky and D. R. Bickel, “Validation of differential gene expression algorithms: Application comparing fold change estimation to hypothesis testing,” BMC Bioinformatics 11, 63 (2010). Article

Gene network reconstruction from transcriptional dynamics

28 March 2009 Leave a comment

D. R. Bickel, Z. Montazeri, P.-C. Hsieh, M. Beatty, S. J. Lawit, and N. J. Bate, “Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: A case for the second derivative,” Bioinformatics 25, 772-779 (2009).

Open access (PDF) | Supplement & software | Data

Local false discovery rate software

5 November 2008 Leave a comment

Zahra Montazeri and David Bickel developed empiricalBayes, an R software bundle that provides a simple solution to the extreme multiple testing problem. It contains two packages:

  • localFDR estimates local false discovery rates given a vector of p-values.
  • HighProbability determines which p-values are low enough that their alternative hypotheses can be considered highly probable.
Categories: software, trainee author