@article {38203, title = {Differential abundance analysis for microbial marker-gene surveys}, journal = {Nature methods}, volume = {10}, year = {2013}, publisher = {Nature Publishing Group}, chapter = {1200}, abstract = {We introduce a methodology to assess differential abundance in sparse high-throughput microbial marker-gene survey data. Our approach, implemented in the metagenomeSeq Bioconductor package, relies on a novel normalization technique and a statistical model that accounts for undersampling{\textemdash}a common feature of large-scale marker-gene studies. Using simulated data and several published microbiota data sets, we show that metagenomeSeq outperforms the tools currently used in this field.}, isbn = {1548-7091}, doi = {10.1038/nmeth.2658}, url = {http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2658.html}, author = {Joseph N. Paulson and Stine, O. Colin and H{\'e}ctor Corrada Bravo and M. Pop} }