Background correction using dinucleotide affinities improves the performance of GCRMA

BMC Bioinformatics

Table 2 AffyComp scores for GCRMA-L, GCRMA-R and GCRMA-NN

Metric	GCRMA-L	GCRMA-R	GCRMA-NN	Perfect score
Median SD	0.06	0.06	0.07	0
null log-fc IQR	0.05	0.03	0.08	0
null log-fc 99.9%	0.62	0.61	0.64	0
Signal detect slope	0.99	1	0.98	1
Signal detect R²	0.89	0.91	0.91	1
low.slope	0.49	0.48	0.55	1
med.slope	1.05	1.06	1.02	1
high.slope	0.97	0.97	0.96	1
Obs-intended-fc slope	0.99	1	0.98	1
Obs-(low)int-fc slope	0.48	0.47	0.53	1
low AUC	0.44	0.45	0.50	1
med AUC	0.87	0.87	0.86	1
high AUC	0.85	0.86	0.83	1
weighted avg AUC	0.55	0.56	0.59	1

Fourteen AffyComp metrics for the U133 Latin square dataset rounded to two decimal points.
A brief description of each metric is provided under the Methods section.

ISSN: 1471-2105