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Table 3 The mean square errors of estimated gene expression levels for simulated cDNA microarray data with differentially expressed genes inserted under the medium expression levels condition.

From: Evaluating different methods of microarray data normalization

Percentage of DEG   Sinusoid Banana Mixed
  Method 25% Quantile Median 75% Quantile 25% Quantile Median 75% Quantile 25% Quantile Median 75% Quantile
5% Loess 0.00356 0.00373 0.00389 0.00379 0.00392 0.00407 0.05214 0.05234 0.05259
  Splines 0.00354 0.00370 0.00387 0.00379 0.00393 0.00407 0.05237 0.05258 0.05283
  Wavelets 0.00351 0.00368 0.00384 0.00438 0.00450 0.00466 0.05227 0.05247 0.05272
  Kernel 0.03799 0.03816 0.03838 0.17380 0.17441 0.17487 0.18858 0.18882 0.18904
  SVR 0.00337 0.00353 0.00369 0.00357 0.00368 0.00382 0.05034 0.05049 0.05067
10% Loess 0.00709 0.00723 0.00743 0.00758 0.00780 0.00799 0.05483 0.05506 0.05532
  Splines 0.00707 0.00721 0.00741 0.00763 0.00787 0.00805 0.05507 0.05532 0.05556
  Wavelets 0.00705 0.00718 0.00739 0.00858 0.00881 0.00898 0.05497 0.05522 0.05547
  Kernel 0.03837 0.03857 0.03886 0.15366 0.15461 0.15523 0.18801 0.18830 0.18867
  SVR 0.00672 0.00688 0.00707 0.00709 0.00731 0.00750 0.05150 0.05164 0.05183
15% Loess 0.01041 0.01061 0.01094 0.01108 0.01136 0.01165 0.05964 0.05985 0.06012
  Splines 0.01039 0.01060 0.01091 0.01109 0.01136 0.01165 0.05990 0.06013 0.06039
  Wavelets 0.01038 0.01058 0.01089 0.01251 0.01276 0.01310 0.05978 0.06003 0.06029
  Kernel 0.03867 0.03897 0.03927 0.12923 0.13026 0.13111 0.19337 0.19367 0.19414
  SVR 0.00986 0.01006 0.01032 0.01027 0.01056 0.01081 0.05499 0.05526 0.05550
20% Loess 0.01393 0.01418 0.01444 0.01487 0.01519 0.01542 0.06362 0.06398 0.06432
  Splines 0.01393 0.01415 0.01442 0.01486 0.01518 0.01542 0.06390 0.06425 0.06460
  Wavelets 0.01390 0.01414 0.01440 0.01631 0.01666 0.01689 0.06375 0.06410 0.06445
  Kernel 0.03915 0.03957 0.04004 0.12265 0.12366 0.12464 0.19808 0.19858 0.19909
  SVR 0.01310 0.01334 0.01365 0.01365 0.01399 0.01416 0.05809 0.05835 0.05858
40% Loess 0.02772 0.02813 0.02862 0.02969 0.03004 0.03043 0.07856 0.07910 0.07975
  Splines 0.02774 0.02814 0.02861 0.02966 0.03002 0.03038 0.07884 0.07937 0.08002
  Wavelets 0.02771 0.02811 0.02859 0.03012 0.03049 0.03092 0.07873 0.07926 0.07995
  Kernel 0.04195 0.04261 0.04316 0.15640 0.15816 0.16012 0.20368 0.20443 0.20518
  SVR 0.02545 0.02581 0.02614 0.02656 0.02685 0.02724 0.06786 0.06830 0.06862
  1. DEG: Differentially expressed genes