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Table 2 AUCs for 2-sided test of DE. 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 2-sided tests of DE.

From: A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods

 

limma

FC

t-test

Cyber-T

PPLR

mmgMOS

0.903

0.861

0.902

0.919

0.922

MAS5

0.884

0.848

0.879

0.905

 

CP

0.905

0.873

0.898

0.919

0.889

PLIER

0.898

0.889

0.889

0.911

 

RMA

0.881

0.885

0.858

0.886

0.860

GCRMA

0.890

0.902

0.883

0.909

 

DFW

0.764

0.815

0.732

0.703

0.806

MBEI

0.885

0.884

0.870

0.897

0.855

FARMS

0.842

0.891

0.805

0.844

0.772