Table 1.

Pairwise correlation between ratios estimates for the loop design

Method 1	Method 2	T3/T1	T4/T1	T5/T1	T6/T1	Mean
lmbr/lmbr_dye	limmaQual	0.9966	0.9998	0.9648	0.9909	0.9880
lmbr/lmbr_dye	anovaFix	0.9899	0.9913	0.9721	0.9856	0.9848
lmbr/lmbr_dye	anovaMix	0.9829	0.9751	0.9420	0.9549	0.9637
limmaQual	anovaFix	0.9889	0.9918	0.9298	0.9775	0.9720
limmaQual	anovaMix	0.9810	0.9758	0.8950	0.9467	0.9496
anovaFix	anovaMix	0.9936	0.9847	0.9726	0.9694	0.9801

Correlation between ratios estimated by each pair of applied methods (column 1 and column 2) for a loop design. Each ratio corresponds to a time dependent change in expression as compared to the first time point (T1). The last column corresponds to the mean correlation of the 4 estimates. 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.