Table 6.

Effect of additional normalization procedures on estimating gene profiles from both the interwoven design and the loop design

	Interwoven design
Normalization methods	lmbr	lmbr_dye	limmaQual	anovaFix	anovaMix
none/quantile	0.9602	0.9576	0.9599	0.9605	0.9584
none/scale	0.9900	0.9881	0.9914	0.9867	0.9848
scale/quantile	0.9540	0.9531	0.9557	0.9547	0.9566
	Loop design
	lmbr	lmbr_dye	limmaQual	anovaFix	anovaMix
none/quantile	0.9520	0.9520	0.9534	0.9601	0.9481
none/scale	0.9822	0.9822	0.9793	0.9835	0.9778
scale/quantile	0.9355	0.9355	0.9361	0.9433	0.9370

Similarities between profiles were assessed using the mean cosine similarity measure. Rows indicate the different normalization procedures. Columns indicate the different models used to reconstruct the profiles.