puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis

BMC Bioinformatics

Table 2 Area under ROC curves from different methods for Exon array data

Gene expression estimation methods are combined with different finding-DE-gene methods. PPLR and IPPLR require a level of uncertainty associated with expression estimation, and they are therefore combined with GME and RMA since these two methods can provide variance of gene expression measurements. For t-test we use only the point estimates of gene expression. PLIER provides only a point estimate for gene expression and we only evaluate it combining with t-test. The number after PPLR indicates the sample number used in the importance sampling of the algorithm. The best result for each comparison is highlighted in bold.

ISSN: 1471-2105