Table 3.

Mean similarity between profiles after filtering for both the interwoven and the loop design

	Interwoven design				Loop design
	lmbr	lmbr_dye	limmaQual	anovaFix	lmbr/lmbr_dye	limmaQual	anovaFix
lmbr_dye	0.9834				1.0000
limmaQual	0.9980	0.9799			0.9920
anovaFix	0.9800	0.9948	0.9755		0.9961	0.9851
anovaMix	0.9748	0.9905	0.9701	0.9957	0.9866	0.9728	0.9905

Mean profile similarity using a filtering threshold of 0.4 on all profiles estimated by each of the methods. A pairwise similarity comparison is made for all profile pairs (corresponding to the same gene) estimated by each of the two methods compared, for which at least one profile is above the filtering threshold.