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Table 4 The mean square errors of estimated gene expression levels for simulated cDNA microarray data with differentially expressed genes inserted under the high expression levels conditions.

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 0.00038 0.00039 0.00040 0.00081 0.00087 0.00094 0.04633 0.04639 0.04648
  Splines 0.00035 0.00036 0.00037 0.00079 0.00086 0.00092 0.04658 0.04665 0.04674
  Wavelets 0.00033 0.00034 0.00035 0.00115 0.00121 0.00129 0.04643 0.04650 0.04660
  Kernel 0.03781 0.03782 0.03783 0.16417 0.16453 0.16513 0.17428 0.17436 0.17447
  SVR 0.00031 0.00032 0.00033 0.00080 0.00087 0.00092 0.04527 0.04534 0.04544
10% Loess 0.00146 0.00153 0.00168 0.00145 0.00156 0.00167 0.04733 0.04748 0.04758
  Splines 0.00142 0.00149 0.00160 0.00147 0.00157 0.00168 0.04756 0.04767 0.04779
  Wavelets 0.00140 0.00147 0.00159 0.00160 0.00170 0.00182 0.04725 0.04736 0.04748
  Kernel 0.02662 0.03454 0.03789 0.23086 0.23135 0.23245 0.18441 0.19003 0.19176
  SVR 0.00126 0.00133 0.00144 0.00142 0.00154 0.00166 0.04678 0.04687 0.04696
15% Loess 0.00203 0.00217 0.00234 0.00199 0.00212 0.00224 0.04963 0.04976 0.04991
  Splines 0.00198 0.00211 0.00223 0.00200 0.00211 0.00222 0.04987 0.05001 0.05014
  Wavelets 0.00196 0.00209 0.00224 0.00219 0.00240 0.00257 0.04975 0.04989 0.05001
  Kernel 0.02318 0.02992 0.03729 0.17578 0.20066 0.22763 0.18472 0.18898 0.18923
  SVR 0.00178 0.00190 0.00200 0.00170 0.00180 0.00189 0.04885 0.04898 0.04912
20% Loess 0.00260 0.00275 0.00293 0.00259 0.00272 0.00289 0.04917 0.04930 0.04944
  Splines 0.00254 0.00268 0.00286 0.00260 0.00270 0.00289 0.04933 0.04946 0.04961
  Wavelets 0.00253 0.00267 0.00284 0.00289 0.00304 0.00320 0.04919 0.04933 0.04947
  Kernel 0.02224 0.02819 0.03468 0.16500 0.17817 0.20385 0.18207 0.18716 0.19141
  SVR 0.00226 0.00239 0.00255 0.00247 0.00258 0.00272 0.04839 0.04850 0.04863
40% Loess 0.00501 0.00520 0.00545 0.00518 0.00538 0.00555 0.04980 0.04999 0.05020
  Splines 0.00498 0.00519 0.00539 0.00520 0.00538 0.00558 0.05002 0.05022 0.05038
  Wavelets 0.00496 0.00517 0.00537 0.00535 0.00551 0.00572 0.04984 0.05004 0.05020
  Kernel 0.02155 0.02487 0.02810 0.18250 0.20140 0.22296 0.17524 0.18072 0.18433
  SVR 0.00446 0.00467 0.00489 0.00464 0.00483 0.00505 0.04809 0.04829 0.04860
  1. DEG: Differentially expressed genes