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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.
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BMC Bioinformatics

ISSN: 1471-2105

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