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Table 6 Effect of additional normalization procedures on estimating gene profiles from both the interwoven design and the loop design

From: Evaluation of time profile reconstruction from complex two-color microarray designs

  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
  1. 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.