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Table 5 Leave-one-out cross-validation k-NN error rates for location normalized data. For each data set, the normalization methods were ranked based on their LOOCV classification error rates ("Rank"). The smaller the LOOCV classification error rate, the lower the rank. The methods are arranged in the following order: single-bias-removal methods (block 1), double-bias-removal methods (block 2) and the qspline-related methods (block 3). For a given data set, the smallest error rate(s) and rank(s) are shown in bold. The methods and data sets are described in Tables 1, 2 and 4, respectively.

From: Evaluation of normalization methods for cDNA microarray data by k-NN classification

Location Normalization method LIVER CANCER LYMPHOMA RENAL CELL CARCINOMA GASTRIC CARCINOMA LUNG CANCER
  Error Rate Rank Error Rate Rank Error Rate Rank Error Rate Rank Error Rate Rank
N ONRM 0.202 24 0.266 23 0.237 24 0.0347 24 0.359 23.5
GMEDIAN 0.163 21 0.247 21 0.158 22 0.0270 23 0.342 20.5
SL LOESS 0.136 9.5 0.272 24 0.132 16.5 0.0154 12 0.350 22
SL FILTERW3 0.155 16 0.216 20 0.132 16.5 0.0190 14 0.359 23.5
SL FILTERW7 0.144 12.5 0.253 22 0.132 16.5 0.0228 16 0.325 17.5
IG LOESS 0.133 8 0.186 15.5 0.132 16.5 0.0231 20 0.342 20.5
IL LOESS 0.110 2 0.154 13 0.132 16.5 0.0231 20 0.275 12.5
IST SPLINE 0.129 7 0.177 14 0.114 7 0.0153 10 0.334 19
IG SG LOESS 0.136 9.5 0.130 10 0.132 16.5 0 2 0.283 15
IG LOESS-SL LOESS 0.113 3.5 0.117 6.5 0.119 10 0.0154 12 0.242 8.5
IL LOESS-SL LOESS 0.105 1 0.111 4 0.132 16.5 0.0193 15 0.267 10
IG LOESS-LFILTERW3 0.158 19.5 0.136 11 0.092 1.5 0.0231 20 0.242 8.5
IG LOESS-SL FILTERW7 0.113 3.5 0.111 4 0.119 10 0.0154 12 0.217 4
IST SPLINE-SL LOESS 0.121 6 0.102 1 0.119 10 0.0233 22 0.192 1
IST SPLINE-SL FILTERW3 0.157 18 0.139 12 0.092 1.5 0.0229 17.5 0.209 2.5
IIST SPLINE-SL FILTERW7 0.118 5 0.127 9 0.132 16.5 0.0229 17.5 0.209 2.5
Q SPLINEG 0.158 19.5 0.192 17.5 0.096 3.5 0 2 0.275 12.5
QS PLINER 0.166 22 0.123 8 0.096 3.5 0 2 0.275 12.5
Q SPLINEG-SL LOESS 0.138 11 0.198 19 0.119 10 0.00769 7.5 0.225 6
Q SPLINEG-SL FILTERW3 0.144 12.5 0.186 15.5 0.172 23 0.00758 5 0.317 16
Q SPLINEG-SL FILTERW7 0.149 14 0.192 17.5 0.106 6 0.00758 5 0.225 6
QS PLINER-SL LOESS 0.155 16 0.105 2 0.105 5 0.00769 7.5 0.225 6
QS PLINER-SL FILTERW3 0.155 16 0.111 4 0.145 21 0.00758 5 0.325 17.5
QS PLINER-SL FILTERW7 0.169 23 0.117 6.5 0.119 10 0.0114 9 0.275 12.5