Table 3

AUCs for 1-sided test of up-regulation. This table shows AUC values for different combinations of summarization and DE detection methods. The 10 highest AUC values are highlighted in bold. Note that the PPLR method is only applicable to summarization methods that give uncertainty estimates as well as mean expression levels for each probeset. These results were calculated using only the equal spike-ins as true negatives, and all spike-ins with FC > 1 as true positives. A post-summarization loess normalization using the equal-valued spike-ins was used. The results in this table are for 1-sided tests of up-regulation.

limma

FC

t-test

Cyber-T

PPLR

mmgMOS

0.940

0.920

0.938

0.949

0.951

MAS5

0.924

0.908

0.921

0.934

CP

0.940

0.928

0.935

0.948

0.932

PLIER

0.934

0.929

0.930

0.941

RMA

0.929

0.932

0.914

0.932

0.917

GCRMA

0.926

0.946

0.921

0.944

DFW

0.817

0.918

0.794

0.830

0.912

MBEI

0.928

0.928

0.920

0.934

0.915

FARMS

0.883

0.938

0.847

0.908

0.893

Pearson BMC Bioinformatics 2008 9:164   doi:10.1186/1471-2105-9-164