Table 2.

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

	Interwoven design				Loop design
	lmbr	lmbr_dye	limmaQual	anovaFix	lmbr/lmbr_dye	limmaQual	anovaFix
lmbr_dye	0.9477				1.0000
limmaQual	0.9940	0.9359			0.9844
anovaFix	0.9321	0.9572	0.9157		0.9514	0.9252
anovaMix	0.9138	0.9373	0.8989	0.9767	0.9186	0.8934	0.9611

Values in the table correspond to the similarity between any two methods, expressed as the mean profile similarity of the genes. Since the loop design is balanced with respect to the dyes, the results for lmbr and lmbr_dye were the same (see 'Methods' section), which is why they are not treated differently. No filtering applied and similarity is assessed for all 2999 profile estimates.